From 73a9246159a2e9e91e1082f65990ce7e714d8f16 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Fri, 10 May 2024 16:20:13 -0700 Subject: [PATCH 1/4] complete the mixin hierarchy --- biolink-model.yaml | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/biolink-model.yaml b/biolink-model.yaml index 634fd8b11..5003a3601 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -3416,7 +3416,8 @@ slots: - translator_minimal condition promoted by: - is_a: likelihood affected by + mixin: true + is_a: related to at instance level inverse: promotes condition domain: disease or phenotypic feature range: chemical or drug or treatment @@ -3591,18 +3592,24 @@ slots: tested by clinical trials of: is_a: treated in studies by + mixins: + - subject of treatment application or study for treatment by inverse: in clinical trials for domain: disease or phenotypic feature range: chemical or drug or treatment treated in studies by: is_a: treated by + mixins: + - subject of treatment application or study for treatment by inverse: studied to treat domain: disease or phenotypic feature range: chemical or drug or treatment tested by preclinical trials of: is_a: treated in studies by + mixins: + - subject of treatment application or study for treatment by inverse: in preclinical trials for domain: disease or phenotypic feature range: chemical or drug or treatment @@ -3647,6 +3654,8 @@ slots: models demonstrating benefits for: is_a: tested by preclinical trials of + mixins: + - subject of treatment application or study for treatment by inverse: beneficial in models for domain: disease or phenotypic feature range: chemical or drug or treatment @@ -3676,6 +3685,8 @@ slots: treatment applications from: is_a: related to at instance level + mixins: + - subject of treatment application or study for treatment by inverse: applied to treat domain: disease or phenotypic feature range: chemical or drug or treatment From 20454199eebce91d32df14a84ec9f3e8eab79dcd Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Fri, 10 May 2024 16:27:37 -0700 Subject: [PATCH 2/4] regenerate viz --- biolink-model.yaml | 2 +- src/biolink_model/schema/biolink_model.yaml | 13 +- src/docs/predicates.json | 144 +++++++++++++++++++- src/docs/treats_dagre.json | 7 + 4 files changed, 160 insertions(+), 6 deletions(-) diff --git a/biolink-model.yaml b/biolink-model.yaml index 5003a3601..7ebdc653d 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -3634,7 +3634,7 @@ slots: beneficial in models for: is_a: in preclinical trials for description: >- - Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, + Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity has been shown to be effective in alleviating, preventing, or delaying symptoms/ phenotypes associated with a disease, in a model system for that disease (e.g. a mouse, fly, cell line, etc). notes: >- diff --git a/src/biolink_model/schema/biolink_model.yaml b/src/biolink_model/schema/biolink_model.yaml index 634fd8b11..5003a3601 100644 --- a/src/biolink_model/schema/biolink_model.yaml +++ b/src/biolink_model/schema/biolink_model.yaml @@ -3416,7 +3416,8 @@ slots: - translator_minimal condition promoted by: - is_a: likelihood affected by + mixin: true + is_a: related to at instance level inverse: promotes condition domain: disease or phenotypic feature range: chemical or drug or treatment @@ -3591,18 +3592,24 @@ slots: tested by clinical trials of: is_a: treated in studies by + mixins: + - subject of treatment application or study for treatment by inverse: in clinical trials for domain: disease or phenotypic feature range: chemical or drug or treatment treated in studies by: is_a: treated by + mixins: + - subject of treatment application or study for treatment by inverse: studied to treat domain: disease or phenotypic feature range: chemical or drug or treatment tested by preclinical trials of: is_a: treated in studies by + mixins: + - subject of treatment application or study for treatment by inverse: in preclinical trials for domain: disease or phenotypic feature range: chemical or drug or treatment @@ -3647,6 +3654,8 @@ slots: models demonstrating benefits for: is_a: tested by preclinical trials of + mixins: + - subject of treatment application or study for treatment by inverse: beneficial in models for domain: disease or phenotypic feature range: chemical or drug or treatment @@ -3676,6 +3685,8 @@ slots: treatment applications from: is_a: related to at instance level + mixins: + - subject of treatment application or study for treatment by inverse: applied to treat domain: disease or phenotypic feature range: chemical or drug or treatment diff --git a/src/docs/predicates.json b/src/docs/predicates.json index 0111ab16f..f1f939484 100644 --- a/src/docs/predicates.json +++ b/src/docs/predicates.json @@ -338,6 +338,10 @@ "name": "completed_by", "parent": "related_to_at_instance_level" }, + { + "name": "condition_promoted_by", + "parent": "related_to_at_instance_level" + }, { "name": "contains_process", "parent": "related_to_at_instance_level" @@ -719,10 +723,6 @@ { "name": "condition_predisposed_by", "parent": "likelihood_affected_by" - }, - { - "name": "condition_promoted_by", - "parent": "likelihood_affected_by" } ] }, @@ -986,6 +986,80 @@ } ] }, + { + "name": "subject_of_treatment_application_or_study_for_treatment_by", + "parent": "related_to_at_instance_level", + "children": [ + { + "name": "models_demonstrating_benefits_for", + "parent": "subject_of_treatment_application_or_study_for_treatment_by" + }, + { + "name": "tested_by_clinical_trials_of", + "parent": "subject_of_treatment_application_or_study_for_treatment_by" + }, + { + "name": "tested_by_preclinical_trials_of", + "parent": "subject_of_treatment_application_or_study_for_treatment_by", + "children": [ + { + "name": "models_demonstrating_benefits_for", + "parent": "tested_by_preclinical_trials_of" + } + ] + }, + { + "name": "treated_by", + "parent": "subject_of_treatment_application_or_study_for_treatment_by", + "children": [ + { + "name": "treated_in_studies_by", + "parent": "treated_by", + "children": [ + { + "name": "tested_by_clinical_trials_of", + "parent": "treated_in_studies_by" + }, + { + "name": "tested_by_preclinical_trials_of", + "parent": "treated_in_studies_by", + "children": [ + { + "name": "models_demonstrating_benefits_for", + "parent": "tested_by_preclinical_trials_of" + } + ] + } + ] + } + ] + }, + { + "name": "treated_in_studies_by", + "parent": "subject_of_treatment_application_or_study_for_treatment_by", + "children": [ + { + "name": "tested_by_clinical_trials_of", + "parent": "treated_in_studies_by" + }, + { + "name": "tested_by_preclinical_trials_of", + "parent": "treated_in_studies_by", + "children": [ + { + "name": "models_demonstrating_benefits_for", + "parent": "tested_by_preclinical_trials_of" + } + ] + } + ] + }, + { + "name": "treatment_applications_from", + "parent": "subject_of_treatment_application_or_study_for_treatment_by" + } + ] + }, { "name": "target_for", "parent": "related_to_at_instance_level" @@ -1027,6 +1101,68 @@ { "name": "treatment_applications_from", "parent": "related_to_at_instance_level" + }, + { + "name": "treats_or_applied_or_studied_to_treat", + "parent": "related_to_at_instance_level", + "children": [ + { + "name": "applied_to_treat", + "parent": "treats_or_applied_or_studied_to_treat" + }, + { + "name": "beneficial_in_models_for", + "parent": "treats_or_applied_or_studied_to_treat" + }, + { + "name": "in_clinical_trials_for", + "parent": "treats_or_applied_or_studied_to_treat" + }, + { + "name": "in_preclinical_trials_for", + "parent": "treats_or_applied_or_studied_to_treat", + "children": [ + { + "name": "beneficial_in_models_for", + "parent": "in_preclinical_trials_for" + } + ] + }, + { + "name": "studied_to_treat", + "parent": "treats_or_applied_or_studied_to_treat", + "children": [ + { + "name": "in_clinical_trials_for", + "parent": "studied_to_treat" + }, + { + "name": "in_preclinical_trials_for", + "parent": "studied_to_treat", + "children": [ + { + "name": "beneficial_in_models_for", + "parent": "in_preclinical_trials_for" + } + ] + } + ] + }, + { + "name": "treats", + "parent": "treats_or_applied_or_studied_to_treat", + "children": [ + { + "name": "ameliorates_condition", + "parent": "treats" + }, + { + "name": "preventative_for_condition", + "parent": "treats" + } + ] + } + ] } ] } diff --git a/src/docs/treats_dagre.json b/src/docs/treats_dagre.json index 2ee1c5204..5a45accbc 100644 --- a/src/docs/treats_dagre.json +++ b/src/docs/treats_dagre.json @@ -480,6 +480,13 @@ "target": "applied to treat" } }, + { + "data": { + "id": "related to at instance level-treats or applied or studied to treat", + "source": "related to at instance level", + "target": "treats or applied or studied to treat" + } + }, { "data": { "id": "related to at instance level-temporally related to", From 2c36f2662a0e6b04c8e0717b70e84cd95aa2b5a9 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Fri, 10 May 2024 16:28:55 -0700 Subject: [PATCH 3/4] fix likelhood parents --- biolink-model.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/biolink-model.yaml b/biolink-model.yaml index 7ebdc653d..57b665cad 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -3403,7 +3403,7 @@ slots: promotes condition: mixin: true - is_a: related to at instance level + is_a: affects likelihood of description: >- Holds between a substance, procedure, or activity and a medical condition (disease or phenotypic feature), and states that the substance, procedure, or activity is able to promote it manifesting in the first place. @@ -3417,7 +3417,7 @@ slots: condition promoted by: mixin: true - is_a: related to at instance level + is_a: likelihood affected by inverse: promotes condition domain: disease or phenotypic feature range: chemical or drug or treatment From 9dc33fd581386f73e2e7d5dc02da3dd275ee8db2 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Fri, 10 May 2024 16:37:34 -0700 Subject: [PATCH 4/4] generate changes --- project/jsonld/biolink_model.context.jsonld | 2 +- project/jsonld/biolink_model.jsonld | 26 +- project/owl/biolink_model.owl.ttl | 5617 +-- project/shacl/biolink_model.shacl.ttl | 37358 +++++++++--------- src/biolink_model/datamodel/model.py | 2 +- src/biolink_model/schema/biolink_model.yaml | 6 +- src/biolink_model/scripts/classprefixes.py | 2 +- 7 files changed, 21517 insertions(+), 21496 deletions(-) diff --git a/project/jsonld/biolink_model.context.jsonld b/project/jsonld/biolink_model.context.jsonld index ad45d7e02..fab136b88 100644 --- a/project/jsonld/biolink_model.context.jsonld +++ b/project/jsonld/biolink_model.context.jsonld @@ -1,7 +1,7 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2024-05-10T23:03:10", + "generation_date": "2024-05-10T16:31:05", "source": "biolink_model.yaml" }, "@context": { diff --git a/project/jsonld/biolink_model.jsonld b/project/jsonld/biolink_model.jsonld index a1d0ac776..5d7889a89 100644 --- a/project/jsonld/biolink_model.jsonld +++ b/project/jsonld/biolink_model.jsonld @@ -7688,7 +7688,7 @@ "translator_minimal" ], "from_schema": "https://w3id.org/biolink/biolink-model", - "is_a": "related_to_at_instance_level", + "is_a": "affects_likelihood_of", "mixin": true, "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/promotes_condition", @@ -7704,6 +7704,7 @@ "definition_uri": "https://w3id.org/biolink/vocab/condition_promoted_by", "from_schema": "https://w3id.org/biolink/biolink-model", "is_a": "likelihood_affected_by", + "mixin": true, "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/condition_promoted_by", "multivalued": true, @@ -7979,6 +7980,9 @@ "definition_uri": "https://w3id.org/biolink/vocab/tested_by_clinical_trials_of", "from_schema": "https://w3id.org/biolink/biolink-model", "is_a": "treated_in_studies_by", + "mixins": [ + "subject_of_treatment_application_or_study_for_treatment_by" + ], "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/tested_by_clinical_trials_of", "multivalued": true, @@ -7994,6 +7998,9 @@ "definition_uri": "https://w3id.org/biolink/vocab/treated_in_studies_by", "from_schema": "https://w3id.org/biolink/biolink-model", "is_a": "treated_by", + "mixins": [ + "subject_of_treatment_application_or_study_for_treatment_by" + ], "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/treated_in_studies_by", "multivalued": true, @@ -8009,6 +8016,9 @@ "definition_uri": "https://w3id.org/biolink/vocab/tested_by_preclinical_trials_of", "from_schema": "https://w3id.org/biolink/biolink-model", "is_a": "treated_in_studies_by", + "mixins": [ + "subject_of_treatment_application_or_study_for_treatment_by" + ], "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/tested_by_preclinical_trials_of", "multivalued": true, @@ -8057,7 +8067,7 @@ "@type": "Annotation" } ], - "description": "Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity has been shown to be effective in alleviating, preventing, or delaying symptoms/ phenotypes associated with a disease, in a model system for that disease (e.g. a mouse, fly, cell line, etc).", + "description": "Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity has been shown to be effective in alleviating, preventing, or delaying symptoms/ phenotypes associated with a disease, in a model system for that disease (e.g. a mouse, fly, cell line, etc).", "notes": [ "This predicate would be used to represent Model Organism Database (MOD) records reporting that an intervention alleviated phenotypes associated with a human disease in a model organism designated as a model of that disease. (e.g. a ZFIN record reporting that treatment with Braf Inhibitors reduced the abnormal brain cell proliferation phenotype of zebrafish used to model the human disease Kabuki Syndrome) ." ], @@ -8083,6 +8093,9 @@ "definition_uri": "https://w3id.org/biolink/vocab/models_demonstrating_benefits_for", "from_schema": "https://w3id.org/biolink/biolink-model", "is_a": "tested_by_preclinical_trials_of", + "mixins": [ + "subject_of_treatment_application_or_study_for_treatment_by" + ], "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/models_demonstrating_benefits_for", "multivalued": true, @@ -8134,6 +8147,9 @@ "definition_uri": "https://w3id.org/biolink/vocab/treatment_applications_from", "from_schema": "https://w3id.org/biolink/biolink-model", "is_a": "related_to_at_instance_level", + "mixins": [ + "subject_of_treatment_application_or_study_for_treatment_by" + ], "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/treatment_applications_from", "multivalued": true, @@ -35037,9 +35053,9 @@ ], "metamodel_version": "1.7.0", "source_file": "biolink_model.yaml", - "source_file_date": "2024-05-10T23:03:07", - "source_file_size": 393015, - "generation_date": "2024-05-10T23:03:12", + "source_file_date": "2024-05-10T16:31:01", + "source_file_size": 393418, + "generation_date": "2024-05-10T16:31:06", "@type": "SchemaDefinition", "@context": [ "project/jsonld/biolink_model.context.jsonld", diff --git a/project/owl/biolink_model.owl.ttl b/project/owl/biolink_model.owl.ttl index ca2ea2f90..fd6962a85 100644 --- a/project/owl/biolink_model.owl.ttl +++ b/project/owl/biolink_model.owl.ttl @@ -996,7 +996,8 @@ biolink:models_demonstrating_benefits_for a owl:ObjectProperty ; rdfs:label "models demonstrating benefits for" ; rdfs:domain biolink:DiseaseOrPhenotypicFeature ; rdfs:range biolink:ChemicalOrDrugOrTreatment ; - rdfs:subPropertyOf biolink:tested_by_preclinical_trials_of ; + rdfs:subPropertyOf biolink:subject_of_treatment_application_or_study_for_treatment_by, + biolink:tested_by_preclinical_trials_of ; owl:inverseOf biolink:beneficial_in_models_for ; skos:inScheme . @@ -1433,7 +1434,8 @@ biolink:tested_by_clinical_trials_of a owl:ObjectProperty ; rdfs:label "tested by clinical trials of" ; rdfs:domain biolink:DiseaseOrPhenotypicFeature ; rdfs:range biolink:ChemicalOrDrugOrTreatment ; - rdfs:subPropertyOf biolink:treated_in_studies_by ; + rdfs:subPropertyOf biolink:subject_of_treatment_application_or_study_for_treatment_by, + biolink:treated_in_studies_by ; owl:inverseOf biolink:in_clinical_trials_for ; skos:inScheme . @@ -1448,7 +1450,8 @@ biolink:treatment_applications_from a owl:ObjectProperty ; rdfs:label "treatment applications from" ; rdfs:domain biolink:DiseaseOrPhenotypicFeature ; rdfs:range biolink:ChemicalOrDrugOrTreatment ; - rdfs:subPropertyOf biolink:related_to_at_instance_level ; + rdfs:subPropertyOf biolink:related_to_at_instance_level, + biolink:subject_of_treatment_application_or_study_for_treatment_by ; owl:inverseOf biolink:applied_to_treat ; skos:inScheme . @@ -1663,7 +1666,7 @@ biolink:beneficial_in_models_for a owl:ObjectProperty ; rdfs:range biolink:DiseaseOrPhenotypicFeature ; rdfs:subPropertyOf biolink:in_preclinical_trials_for, biolink:treats_or_applied_or_studied_to_treat ; - skos:definition "Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity has been shown to be effective in alleviating, preventing, or delaying symptoms/ phenotypes associated with a disease, in a model system for that disease (e.g. a mouse, fly, cell line, etc)." ; + skos:definition "Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity has been shown to be effective in alleviating, preventing, or delaying symptoms/ phenotypes associated with a disease, in a model system for that disease (e.g. a mouse, fly, cell line, etc)." ; skos:editorialNote "This predicate would be used to represent Model Organism Database (MOD) records reporting that an intervention alleviated phenotypes associated with a human disease in a model organism designated as a model of that disease. (e.g. a ZFIN record reporting that treatment with Braf Inhibitors reduced the abnormal brain cell proliferation phenotype of zebrafish used to model the human disease Kabuki Syndrome) ." ; skos:inScheme ; biolink:canonical_predicate true . @@ -2496,14 +2499,6 @@ biolink:subclass_of a owl:ObjectProperty ; rdfs:subPropertyOf ; biolink:canonical_predicate true . -biolink:subject_of_treatment_application_or_study_for_treatment_by a owl:ObjectProperty ; - rdfs:label "subject of treatment application or study for treatment by" ; - rdfs:domain biolink:ChemicalOrDrugOrTreatment ; - rdfs:range biolink:DiseaseOrPhenotypicFeature ; - rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:treats_or_applied_or_studied_to_treat ; - skos:inScheme . - biolink:symbol_type a rdfs:Datatype ; owl:equivalentClass xsd:string . @@ -2520,7 +2515,8 @@ biolink:tested_by_preclinical_trials_of a owl:ObjectProperty ; rdfs:label "tested by preclinical trials of" ; rdfs:domain biolink:DiseaseOrPhenotypicFeature ; rdfs:range biolink:ChemicalOrDrugOrTreatment ; - rdfs:subPropertyOf biolink:treated_in_studies_by ; + rdfs:subPropertyOf biolink:subject_of_treatment_application_or_study_for_treatment_by, + biolink:treated_in_studies_by ; owl:inverseOf biolink:in_preclinical_trials_for ; skos:inScheme . @@ -2602,15 +2598,15 @@ biolink:AccessibleDnaRegion a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], biolink:RegulatoryRegion ; skos:altLabel "atac-seq accessible region", "dnase-seq accessible region" ; @@ -2657,31 +2653,31 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity ontogenic association" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; skos:definition "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; skos:inScheme . @@ -2689,32 +2685,32 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity part of association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; skos:definition "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; skos:inScheme . @@ -2730,26 +2726,26 @@ biolink:Bacterium a owl:Class ; biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; rdfs:label "behavior to behavioral feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Behavior ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Behavior ; + owl:allValuesFrom biolink:BehavioralFeature ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:BehavioralFeature ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; skos:inScheme . @@ -2777,20 +2773,20 @@ biolink:BioticExposure a owl:Class ; biolink:Book a owl:Class ; rdfs:label "book" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], + owl:minCardinality 0 ; + owl:onProperty biolink:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:type ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:type ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], biolink:Publication ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; skos:inScheme . @@ -2805,10 +2801,10 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "case to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CaseToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:CaseToEntityAssociationMixin ], biolink:Association ; skos:definition "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." ; skos:inScheme . @@ -2816,16 +2812,13 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; biolink:CausalGeneToDiseaseAssociation a owl:Class ; rdfs:label "causal gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; @@ -2834,10 +2827,13 @@ biolink:CausalGeneToDiseaseAssociation a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -2931,6 +2927,12 @@ biolink:Cell a owl:Class ; biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "cell line as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; @@ -2939,12 +2941,6 @@ biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; skos:inScheme . @@ -2957,167 +2953,167 @@ biolink:CellLineToEntityAssociationMixin a owl:Class ; biolink:ChemicalAffectsGeneAssociation a owl:Class ; rdfs:label "chemical affects gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_part_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_context_qualifier ], biolink:Association ; skos:definition "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; skos:inScheme . @@ -3125,17 +3121,14 @@ biolink:ChemicalAffectsGeneAssociation a owl:Class ; biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; rdfs:label "chemical entity assesses named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], @@ -3143,55 +3136,58 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:inScheme . biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; rdfs:label "chemical entity or gene or gene product regulates gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "A regulatory relationship between two genes" ; skos:inScheme . @@ -3199,32 +3195,20 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; biolink:ChemicalGeneInteractionAssociation a owl:Class ; rdfs:label "chemical gene interaction association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object_context_qualifier ], @@ -3232,74 +3216,86 @@ biolink:ChemicalGeneInteractionAssociation a owl:Class ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_context_qualifier ], biolink:Association ; skos:definition "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; skos:exactMatch SIO:001257 ; @@ -3308,17 +3304,17 @@ biolink:ChemicalGeneInteractionAssociation a owl:Class ; biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical or drug or treatment side effect disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], @@ -3349,37 +3345,37 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; rdfs:label "chemical to chemical derivation association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:catalyst_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:catalyst_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:catalyst_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:ChemicalToChemicalAssociation ; skos:definition "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; @@ -3388,17 +3384,17 @@ biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], @@ -3410,6 +3406,9 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; biolink:ChemicalToPathwayAssociation a owl:Class ; rdfs:label "chemical to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; @@ -3418,18 +3417,15 @@ biolink:ChemicalToPathwayAssociation a owl:Class ; [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An interaction between a chemical entity and a biological process or pathway." ; skos:exactMatch SIO:001250 ; @@ -3479,10 +3475,10 @@ biolink:ClinicalMeasurement a owl:Class ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_attribute_type ], biolink:ClinicalAttribute ; skos:definition "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; @@ -3536,38 +3532,38 @@ biolink:ConceptCountAnalysisResult a owl:Class ; biolink:ContributorAssociation a owl:Class ; rdfs:label "contributor association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Agent ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:InformationContentEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:qualifiers ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:InformationContentEntity ; - owl:onProperty biolink:subject ], + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:qualifiers ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Agent ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; skos:inScheme . @@ -3575,29 +3571,29 @@ biolink:ContributorAssociation a owl:Class ; biolink:CorrelatedGeneToDiseaseAssociation a owl:Class ; rdfs:label "correlated gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -3631,21 +3627,21 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneticInheritance ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; skos:inScheme . @@ -3653,14 +3649,14 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a owl:Class ; rdfs:label "disease or phenotypic feature to location association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], @@ -3683,41 +3679,41 @@ biolink:DiseaseToExposureEventAssociation a owl:Class ; biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "disease to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:onset_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:Onset ; owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:FrequencyQuantifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:object ], biolink:Association ; skos:closeMatch dcid:DiseaseSymptomAssociation ; skos:definition "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; @@ -3769,16 +3765,16 @@ biolink:DrugToEntityAssociationMixin a owl:Class ; biolink:DrugToGeneAssociation a owl:Class ; rdfs:label "drug to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DrugToEntityAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:DrugToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "An interaction between a drug and a gene or gene product." ; @@ -3817,43 +3813,46 @@ biolink:DrugToGeneInteractionExposure a owl:Class ; biolink:DruggableGeneToDiseaseAssociation a owl:Class ; rdfs:label "druggable gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_evidence ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; + owl:onProperty biolink:has_evidence ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; - owl:onProperty biolink:has_evidence ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], biolink:GeneToDiseaseAssociation ; skos:inScheme . biolink:EntityToDiseaseAssociation a owl:Class ; rdfs:label "entity to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:MaxResearchPhaseEnum ; owl:onProperty biolink:max_research_phase ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; + owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:clinical_approval_status ], @@ -3864,11 +3863,8 @@ biolink:EntityToDiseaseAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MaxResearchPhaseEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:max_research_phase ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; - owl:onProperty biolink:clinical_approval_status ], biolink:Association ; skos:inScheme . @@ -3887,22 +3883,22 @@ biolink:EntityToOutcomeAssociationMixin a owl:Class ; biolink:EntityToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "entity to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; - owl:onProperty biolink:clinical_approval_status ], - [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:max_research_phase ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MaxResearchPhaseEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:max_research_phase ], + owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:MaxResearchPhaseEnum ; owl:onProperty biolink:max_research_phase ], biolink:Association ; skos:inScheme . @@ -3944,23 +3940,23 @@ biolink:Event a owl:Class ; biolink:ExonToTranscriptRelationship a owl:Class ; rdfs:label "exon to transcript relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Transcript ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Exon ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Exon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Transcript ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:SequenceFeatureRelationship ; skos:definition "A transcript is formed from multiple exons" ; skos:inScheme . @@ -3973,21 +3969,21 @@ biolink:ExposureEventToOutcomeAssociation a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:time_type ; owl:onProperty biolink:temporal_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:temporal_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:temporal_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:temporal_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:population_context_qualifier ], biolink:Association ; skos:definition "An association between an exposure event and an outcome." ; skos:inScheme . @@ -3995,17 +3991,17 @@ biolink:ExposureEventToOutcomeAssociation a owl:Class ; biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "exposure event to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:ExposureEvent ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ExposureEvent ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; skos:inScheme . @@ -4064,175 +4060,175 @@ biolink:GeneAffectsChemicalAssociation a owl:Class ; rdfs:label "gene affects chemical association" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:object_derivative_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_derivative_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; owl:onProperty biolink:object_part_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:object_context_qualifier ], biolink:Association ; skos:definition "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; skos:inScheme . @@ -4240,60 +4236,60 @@ biolink:GeneAffectsChemicalAssociation a owl:Class ; biolink:GeneAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "gene as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:GeneToDiseaseAssociation ; skos:inScheme . biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; rdfs:label "gene has variant that contributes to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -4563,49 +4559,49 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; rdfs:seeAlso ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:quantifier_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:LifeStage ; owl:onProperty biolink:stage_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:quantifier_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; skos:editorialNote "TBD: introduce subclasses for distinction between wild-type and experimental conditions?" ; @@ -4614,17 +4610,17 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; biolink:GeneToGeneCoexpressionAssociation a owl:Class ; rdfs:label "gene to gene coexpression association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneExpressionMixin ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], biolink:GeneToGeneAssociation ; skos:definition "Indicates that two genes are co-expressed, generally under the same conditions." ; skos:inScheme . @@ -4632,32 +4628,32 @@ biolink:GeneToGeneCoexpressionAssociation a owl:Class ; biolink:GeneToGeneFamilyAssociation a owl:Class ; rdfs:label "gene to gene family association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneFamily ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; skos:inScheme . @@ -4665,32 +4661,32 @@ biolink:GeneToGeneFamilyAssociation a owl:Class ; biolink:GeneToGeneHomologyAssociation a owl:Class ; rdfs:label "gene to gene homology association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:GeneToGeneAssociation ; skos:definition "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; skos:inScheme . @@ -4698,31 +4694,31 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; biolink:GeneToGeneProductRelationship a owl:Class ; rdfs:label "gene to gene product relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneProductMixin ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneProductMixin ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:subject ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is transcribed and potentially translated to a gene product" ; @@ -4731,22 +4727,22 @@ biolink:GeneToGeneProductRelationship a owl:Class ; biolink:GeneToGoTermAssociation a owl:Class ; rdfs:label "gene to go term association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:subject ], biolink:FunctionalAssociation ; skos:altLabel "functional association" ; @@ -4756,17 +4752,8 @@ biolink:GeneToGoTermAssociation a owl:Class ; biolink:GeneToPathwayAssociation a owl:Class ; rdfs:label "gene to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], @@ -4776,6 +4763,15 @@ biolink:GeneToPathwayAssociation a owl:Class ; [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An interaction between a gene or gene product and a biological process or pathway." ; skos:inScheme . @@ -4783,29 +4779,29 @@ biolink:GeneToPathwayAssociation a owl:Class ; biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; skos:exactMatch WBVocab:Gene-Phenotype-Association ; skos:inScheme . @@ -4813,14 +4809,14 @@ biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; biolink:Genome a owl:Class ; rdfs:label "genome" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenomicEntity ], biolink:BiologicalEntity ; skos:closeMatch dcid:GenomeAssemblyUnit ; skos:definition "A genome is the sum of genetic material within a cell or virion." ; @@ -4833,22 +4829,22 @@ biolink:GenomicBackgroundExposure a owl:Class ; rdfs:label "genomic background exposure" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:GeneGroupingMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:ThingWithTaxon ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin ], + owl:someValuesFrom biolink:ExposureEvent ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon ], + owl:someValuesFrom biolink:GenomicEntity ], biolink:Attribute ; skos:definition "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; skos:inScheme . @@ -4856,8 +4852,8 @@ biolink:GenomicBackgroundExposure a owl:Class ; biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "genotype as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -4866,33 +4862,33 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], biolink:GenotypeToDiseaseAssociation ; skos:inScheme . biolink:GenotypeToGeneAssociation a owl:Class ; rdfs:label "genotype to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], @@ -4900,8 +4896,8 @@ biolink:GenotypeToGeneAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; skos:inScheme . @@ -4909,29 +4905,29 @@ biolink:GenotypeToGeneAssociation a owl:Class ; biolink:GenotypeToGenotypePartAssociation a owl:Class ; rdfs:label "genotype to genotype part association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Genotype ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -4942,7 +4938,10 @@ biolink:GenotypeToGenotypePartAssociation a owl:Class ; biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "genotype to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; @@ -4950,21 +4949,18 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; skos:inScheme . @@ -4972,19 +4968,13 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; biolink:GenotypeToVariantAssociation a owl:Class ; rdfs:label "genotype to variant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -4993,8 +4983,14 @@ biolink:GenotypeToVariantAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], @@ -5036,13 +5032,13 @@ biolink:GeographicExposure a owl:Class ; biolink:GeographicLocationAtTime a owl:Class ; rdfs:label "geographic location at time" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:time_type ; + owl:minCardinality 0 ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:time_type ; owl:onProperty biolink:timepoint ], biolink:GeographicLocation ; skos:definition "a location that can be described in lat/long coordinates, for a particular time" ; @@ -5063,14 +5059,14 @@ biolink:GrossAnatomicalStructure a owl:Class ; biolink:Haplotype a owl:Class ; rdfs:label "haplotype" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], biolink:BiologicalEntity ; skos:definition "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; skos:exactMatch , @@ -5102,31 +5098,31 @@ biolink:InformationContentEntityToNamedThingAssociation a owl:Class ; rdfs:label "information content entity to named thing association" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; skos:inScheme . @@ -5205,16 +5201,16 @@ biolink:MacromolecularComplex a owl:Class ; biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ; rdfs:label "macromolecular machine to biological process association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:BiologicalProcess ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalProcess ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], biolink:FunctionalAssociation ; skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; @@ -5223,16 +5219,16 @@ biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ; biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ; rdfs:label "macromolecular machine to cellular component association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:CellularComponent ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:CellularComponent ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:FunctionalAssociation ; skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; @@ -5241,16 +5237,16 @@ biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ; biolink:MacromolecularMachineToMolecularActivityAssociation a owl:Class ; rdfs:label "macromolecular machine to molecular activity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], biolink:FunctionalAssociation ; skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ; @@ -5259,26 +5255,26 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a owl:Class ; biolink:MaterialSampleDerivationAssociation a owl:Class ; rdfs:label "material sample derivation association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -5348,22 +5344,22 @@ biolink:MicroRNA a owl:Class ; biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; rdfs:label "molecular activity to chemical entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularActivity ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; @@ -5373,21 +5369,21 @@ biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; rdfs:label "molecular activity to molecular activity association" ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularActivity ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; @@ -5396,14 +5392,20 @@ biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; biolink:MolecularActivityToPathwayAssociation a owl:Class ; rdfs:label "molecular activity to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Pathway ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -5412,16 +5414,10 @@ biolink:MolecularActivityToPathwayAssociation a owl:Class ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], biolink:Association ; skos:definition "Association that holds the relationship between a reaction and the pathway it participates in." ; skos:inScheme . @@ -5429,77 +5425,77 @@ biolink:MolecularActivityToPathwayAssociation a owl:Class ; biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a owl:Class ; rdfs:label "named thing associated with likelihood of named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:population_context_qualifier ], - [ a owl:Restriction ; owl:allValuesFrom biolink:predicate_type ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:population_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:population_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:population_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme . @@ -5514,13 +5510,13 @@ biolink:NucleosomeModification a owl:Class ; rdfs:label "nucleosome modification" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EpigenomicEntity ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneProductIsoformMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:EpigenomicEntity ], biolink:BiologicalEntity ; skos:definition "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; skos:inScheme . @@ -5534,76 +5530,76 @@ biolink:ObservedExpectedFrequencyAnalysisResult a owl:Class ; biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; rdfs:label "organism taxon to environment association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], biolink:Association ; skos:inScheme . biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; rdfs:label "organism taxon to organism taxon interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:associated_environmental_context ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:associated_environmental_context ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:associated_environmental_context ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:associated_environmental_context ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; skos:inScheme . @@ -5612,30 +5608,30 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; rdfs:label "organism taxon to organism taxon specialization" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:object ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; @@ -5645,16 +5641,16 @@ biolink:OrganismToOrganismAssociation a owl:Class ; rdfs:label "organism to organism association" ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:IndividualOrganism ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:IndividualOrganism ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -5667,16 +5663,16 @@ biolink:OrganismToOrganismAssociation a owl:Class ; biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "organismal entity as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; @@ -5687,50 +5683,50 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; biolink:PairwiseMolecularInteraction a owl:Class ; rdfs:label "pairwise molecular interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:interacting_molecules_category ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:interacting_molecules_category ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:interacting_molecules_category ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:interacting_molecules_category ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:interacting_molecules_category ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:interacting_molecules_category ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:subject ], biolink:PairwiseGeneToGeneInteraction ; skos:definition "An interaction at the molecular level between two physical entities" ; skos:inScheme . @@ -5822,20 +5818,20 @@ biolink:Phenomenon a owl:Class ; biolink:PhenotypicFeatureToDiseaseAssociation a owl:Class ; rdfs:label "phenotypic feature to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], biolink:Association ; skos:inScheme . @@ -5889,20 +5885,23 @@ biolink:Plant a owl:Class ; biolink:PopulationToPopulationAssociation a owl:Class ; rdfs:label "population to population association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], @@ -5910,11 +5909,8 @@ biolink:PopulationToPopulationAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a two populations" ; skos:inScheme . @@ -5932,193 +5928,193 @@ biolink:PredicateMapping a owl:Class ; rdfs:label "predicate mapping" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_part_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:broad_match ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:broad_match ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:narrow_match ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:exact_match ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:broad_match ], + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:narrow_match ], + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:mapped_predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:exact_match ], + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:mapped_predicate ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:broad_match ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:narrow_match ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:broad_match ], + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:mapped_predicate ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], linkml:ClassDefinition ; skos:definition "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; skos:inScheme . @@ -6221,13 +6217,13 @@ biolink:RNAProductIsoform a owl:Class ; biolink:ReactionToCatalystAssociation a owl:Class ; rdfs:label "reaction to catalyst association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], biolink:ReactionToParticipantAssociation ; skos:inScheme . @@ -6236,10 +6232,10 @@ biolink:ReagentTargetedGene a owl:Class ; rdfs:label "reagent targeted gene" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], @@ -6300,12 +6296,12 @@ biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:Treatment ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; skos:inScheme ; @@ -6314,44 +6310,44 @@ biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; biolink:Serial a owl:Class ; rdfs:label "serial" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:type ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; + owl:onProperty biolink:iso_abbreviation ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:type ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:issue ], + owl:minCardinality 0 ; + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:issue ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:volume ], + owl:minCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:volume ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:issue ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:type ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:issue ], @@ -6412,14 +6408,14 @@ biolink:Snv a owl:Class ; biolink:SocioeconomicExposure a owl:Class ; rdfs:label "socioeconomic exposure" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:SocioeconomicAttribute ; + owl:onProperty biolink:has_attribute ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ExposureEvent ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:SocioeconomicAttribute ; - owl:onProperty biolink:has_attribute ], biolink:Attribute ; skos:definition "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; skos:inScheme . @@ -6471,6 +6467,12 @@ biolink:StudyVariable a owl:Class ; biolink:TaxonToTaxonAssociation a owl:Class ; rdfs:label "taxon to taxon association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; @@ -6478,16 +6480,10 @@ biolink:TaxonToTaxonAssociation a owl:Class ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], biolink:Association ; skos:inScheme . @@ -6508,21 +6504,21 @@ biolink:TranscriptToGeneRelationship a owl:Class ; rdfs:label "transcript to gene relationship" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Transcript ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:object ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is a collection of transcripts" ; @@ -6531,9 +6527,6 @@ biolink:TranscriptToGeneRelationship a owl:Class ; biolink:TranscriptionFactorBindingSite a owl:Class ; rdfs:label "transcription factor binding site" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; @@ -6542,7 +6535,10 @@ biolink:TranscriptionFactorBindingSite a owl:Class ; [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], - biolink:RegulatoryRegion ; + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], + biolink:RegulatoryRegion ; skos:altLabel "binding site", "tf binding site" ; skos:definition "A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription" ; @@ -6552,36 +6548,36 @@ biolink:TranscriptionFactorBindingSite a owl:Class ; biolink:VariantAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "variant as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:subject ], biolink:VariantToDiseaseAssociation ; skos:inScheme . biolink:VariantToGeneExpressionAssociation a owl:Class ; rdfs:label "variant to gene expression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneExpressionMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneExpressionMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], biolink:VariantToGeneAssociation ; skos:definition "An association between a variant and expression of a gene (i.e. e-QTL)" ; @@ -6590,19 +6586,19 @@ biolink:VariantToGeneExpressionAssociation a owl:Class ; biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "variant to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme . @@ -6610,56 +6606,56 @@ biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; biolink:VariantToPopulationAssociation a owl:Class ; rdfs:label "variant to population association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQualifierMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_quotient ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_quotient ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_count ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_total ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FrequencyQualifierMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FrequencyQuantifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_total ], @@ -7205,7 +7201,8 @@ biolink:treated_in_studies_by a owl:ObjectProperty ; rdfs:label "treated in studies by" ; rdfs:domain biolink:DiseaseOrPhenotypicFeature ; rdfs:range biolink:ChemicalOrDrugOrTreatment ; - rdfs:subPropertyOf biolink:treated_by ; + rdfs:subPropertyOf biolink:subject_of_treatment_application_or_study_for_treatment_by, + biolink:treated_by ; owl:inverseOf biolink:studied_to_treat ; skos:inScheme . @@ -7236,41 +7233,41 @@ biolink:AdministrativeEntity a owl:Class ; biolink:Article a owl:Class ; rdfs:label "article" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:volume ], + owl:maxCardinality 1 ; + owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:published_in ], + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:issue ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:volume ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:issue ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:iso_abbreviation ], + owl:minCardinality 1 ; + owl:onProperty biolink:published_in ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:issue ], + owl:minCardinality 0 ; + owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:maxCardinality 1 ; owl:onProperty biolink:published_in ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:iso_abbreviation ], biolink:Publication ; skos:definition "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; skos:exactMatch fabio:article, @@ -7281,10 +7278,10 @@ biolink:Behavior a owl:Class ; rdfs:label "behavior" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ActivityAndBehavior ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ActivityAndBehavior ], + owl:someValuesFrom biolink:OntologyClass ], biolink:BiologicalProcess ; skos:exactMatch STY:T053, ; @@ -7303,32 +7300,32 @@ biolink:BehavioralFeature a owl:Class ; biolink:BookChapter a owl:Class ; rdfs:label "book chapter" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:minCardinality 1 ; owl:onProperty biolink:published_in ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:volume ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:chapter ], + owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:chapter ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:published_in ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:chapter ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:published_in ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:volume ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:chapter ], biolink:Publication ; skos:inScheme . @@ -7346,20 +7343,20 @@ biolink:Case a owl:Class ; biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "cell line to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:CellLineToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; skos:inScheme . @@ -7379,14 +7376,14 @@ biolink:ChemicalEntityToEntityAssociationMixin a owl:Class ; biolink:ChemicalExposure a owl:Class ; rdfs:label "chemical exposure" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_quantitative_value ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ExposureEvent ], [ a owl:Restriction ; owl:allValuesFrom biolink:QuantityValue ; owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_quantitative_value ], biolink:Attribute ; skos:definition "A chemical exposure is an intake of a particular chemical entity." ; skos:exactMatch ECTO:9000000, @@ -7396,29 +7393,29 @@ biolink:ChemicalExposure a owl:Class ; biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical or drug or treatment to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:FDA_adverse_event_level ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:FDAIDAAdverseEventEnum ; - owl:onProperty biolink:FDA_adverse_event_level ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:FDA_adverse_event_level ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:FDAIDAAdverseEventEnum ; + owl:onProperty biolink:FDA_adverse_event_level ], biolink:Association ; skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; skos:inScheme . @@ -7544,10 +7541,10 @@ biolink:GeneFamily a owl:Class ; rdfs:label "gene family" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GeneGroupingMixin ], biolink:BiologicalEntity ; skos:altLabel "orthogroup", "protein family" ; @@ -7562,77 +7559,77 @@ biolink:GeneFamily a owl:Class ; biolink:GenomicSequenceLocalization a owl:Class ; rdfs:label "genomic sequence localization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:genome_build ], + owl:allValuesFrom biolink:PhaseEnum ; + owl:onProperty biolink:phase ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:StrandEnum ; - owl:onProperty biolink:strand ], + owl:onProperty biolink:genome_build ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:end_interbase_coordinate ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:genome_build ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:phase ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:strand ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:start_interbase_coordinate ], + owl:onProperty biolink:strand ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:start_interbase_coordinate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:phase ], + owl:allValuesFrom biolink:StrandEnum ; + owl:onProperty biolink:strand ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhaseEnum ; - owl:onProperty biolink:phase ], + owl:allValuesFrom biolink:NucleicAcidEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:phase ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; - owl:onProperty biolink:object ], + owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:strand ], + owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:StrandEnum ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:end_interbase_coordinate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:genome_build ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:start_interbase_coordinate ], + owl:minCardinality 0 ; + owl:onProperty biolink:genome_build ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:NucleicAcidEntity ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:start_interbase_coordinate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:SequenceAssociation ; skos:broadMatch dcid:Chromosome ; skos:definition "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; @@ -7642,38 +7639,38 @@ biolink:GenomicSequenceLocalization a owl:Class ; biolink:GenotypeToDiseaseAssociation a owl:Class ; rdfs:label "genotype to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:object ], biolink:Association ; skos:inScheme ; skos:note "TODO decide no how to model pathogenicity" . @@ -7686,22 +7683,22 @@ biolink:GenotypeToEntityAssociationMixin a owl:Class ; biolink:GeographicLocation a owl:Class ; rdfs:label "geographic location" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:float ; owl:onProperty biolink:longitude ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:latitude ], [ a owl:Restriction ; owl:allValuesFrom xsd:float ; owl:onProperty biolink:latitude ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; + owl:maxCardinality 1 ; owl:onProperty biolink:longitude ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:longitude ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:latitude ], biolink:PlanetaryEntity ; skos:definition "a location that can be described in lat/long coordinates" ; @@ -7747,10 +7744,10 @@ biolink:PairwiseGeneToGeneInteraction a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], biolink:GeneToGeneAssociation ; skos:definition "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; @@ -7761,10 +7758,10 @@ biolink:Polypeptide a owl:Class ; rdfs:label "polypeptide" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], biolink:BiologicalEntity ; skos:altLabel "amino acid entity" ; skos:definition "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; @@ -7776,6 +7773,9 @@ biolink:Polypeptide a owl:Class ; biolink:ReactionToParticipantAssociation a owl:Class ; rdfs:label "reaction to participant association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:reaction_side ], + [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:stoichiometry ], [ a owl:Restriction ; @@ -7783,34 +7783,31 @@ biolink:ReactionToParticipantAssociation a owl:Class ; owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:stoichiometry ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; owl:allValuesFrom biolink:ReactionSideEnum ; owl:onProperty biolink:reaction_side ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:reaction_direction ], + owl:maxCardinality 1 ; + owl:onProperty biolink:reaction_side ], [ a owl:Restriction ; owl:allValuesFrom biolink:ReactionDirectionEnum ; owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:stoichiometry ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:stoichiometry ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:reaction_side ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:reaction_side ], + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:stoichiometry ], biolink:ChemicalToChemicalAssociation ; skos:inScheme . @@ -7842,26 +7839,26 @@ biolink:StudyPopulation a owl:Class ; biolink:Treatment a owl:Class ; rdfs:label "treatment" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_device ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Procedure ; - owl:onProperty biolink:has_procedure ], - [ a owl:Restriction ; owl:allValuesFrom biolink:Device ; owl:onProperty biolink:has_device ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Drug ; + owl:minCardinality 0 ; owl:onProperty biolink:has_drug ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ExposureEvent ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:has_device ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Procedure ; + owl:onProperty biolink:has_procedure ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Drug ; owl:onProperty biolink:has_drug ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_procedure ], @@ -7877,38 +7874,38 @@ biolink:Treatment a owl:Class ; biolink:VariantToDiseaseAssociation a owl:Class ; rdfs:label "variant to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme ; skos:note "TODO decide no how to model pathogenicity" . @@ -7916,26 +7913,26 @@ biolink:VariantToDiseaseAssociation a owl:Class ; biolink:VariantToGeneAssociation a owl:Class ; rdfs:label "variant to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; skos:inScheme . @@ -7955,14 +7952,6 @@ biolink:address a owl:DatatypeProperty ; skos:definition "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; skos:inScheme . -biolink:affects_likelihood_of a owl:DatatypeProperty ; - rdfs:label "affects likelihood of" ; - rdfs:subPropertyOf biolink:related_to_at_instance_level ; - skos:definition "Holds between two entities where the presence or application of one alters the chance that the other will come to be." ; - skos:editorialNote "- This predicate implies causation, where the 'affected' entity is something that does not yet exist, and the actions/execution of effector impact the likelihood that this entity may come to be. It is NOT to be used for a statistical associations that describe correlations between two feature variables (use predicates in the 'associated with likelihood of' hierarchy here.)" ; - skos:inScheme ; - biolink:canonical_predicate true . - biolink:agent_type a owl:ObjectProperty ; rdfs:label "agent type" ; rdfs:domain biolink:Association ; @@ -8403,7 +8392,7 @@ biolink:promotes_condition a owl:ObjectProperty ; rdfs:label "promotes condition" ; rdfs:domain biolink:ChemicalOrDrugOrTreatment ; rdfs:range biolink:DiseaseOrPhenotypicFeature ; - rdfs:subPropertyOf biolink:related_to_at_instance_level ; + rdfs:subPropertyOf biolink:affects_likelihood_of ; skos:definition "Holds between a substance, procedure, or activity and a medical condition (disease or phenotypic feature), and states that the substance, procedure, or activity is able to promote it manifesting in the first place." ; skos:inScheme ; biolink:canonical_predicate true ; @@ -8605,23 +8594,23 @@ biolink:ActivityAndBehavior a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme . @@ -8653,35 +8642,35 @@ biolink:ChemicalRole a owl:Class ; biolink:ChemicalToChemicalAssociation a owl:Class ; rdfs:label "chemical to chemical association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; skos:inScheme . @@ -8760,55 +8749,55 @@ biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme ; skos:narrowMatch WBVocab:Gene-Phenotype-Association, @@ -8864,26 +8853,26 @@ biolink:Onset a owl:Class ; biolink:OrganismTaxonToOrganismTaxonAssociation a owl:Class ; rdfs:label "organism taxon to organism taxon association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:subject ], biolink:Association ; skos:definition "A relationship between two organism taxon nodes" ; skos:inScheme . @@ -8930,17 +8919,17 @@ biolink:ReactionSideEnum a owl:Class ; biolink:RegulatoryRegion a owl:Class ; rdfs:label "regulatory region" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], biolink:BiologicalEntity ; skos:altLabel "regulatory element" ; skos:definition "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene" ; @@ -8976,6 +8965,14 @@ biolink:adjusted_p_value a owl:DatatypeProperty ; skos:definition "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; skos:inScheme . +biolink:affects_likelihood_of a owl:DatatypeProperty ; + rdfs:label "affects likelihood of" ; + rdfs:subPropertyOf biolink:related_to_at_instance_level ; + skos:definition "Holds between two entities where the presence or application of one alters the chance that the other will come to be." ; + skos:editorialNote "- This predicate implies causation, where the 'affected' entity is something that does not yet exist, and the actions/execution of effector impact the likelihood that this entity may come to be. It is NOT to be used for a statistical associations that describe correlations between two feature variables (use predicates in the 'associated with likelihood of' hierarchy here.)" ; + skos:inScheme ; + biolink:canonical_predicate true . + biolink:aggregate_statistic a owl:DatatypeProperty ; rdfs:label "aggregate statistic" ; rdfs:subPropertyOf biolink:node_property ; @@ -9273,14 +9270,14 @@ biolink:CellularComponent a owl:Class ; biolink:DatasetDistribution a owl:Class ; rdfs:label "dataset distribution" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:distribution_download_url ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:distribution_download_url ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:distribution_download_url ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:distribution_download_url ], biolink:InformationContentEntity ; skos:definition "an item that holds distribution level information about a dataset." ; skos:exactMatch dcat:Distribution ; @@ -9291,6 +9288,12 @@ biolink:DatasetSummary a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:source_web_page ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:source_logo ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:source_logo ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:source_web_page ], @@ -9300,12 +9303,6 @@ biolink:DatasetSummary a owl:Class ; [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:source_web_page ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:source_logo ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:source_logo ], biolink:InformationContentEntity ; skos:definition "an item that holds summary level information about a dataset." ; skos:inScheme . @@ -9332,20 +9329,20 @@ biolink:GeneProductIsoformMixin a owl:Class ; biolink:GeneToGeneAssociation a owl:Class ; rdfs:label "gene to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -9430,22 +9427,22 @@ biolink:Protein a owl:Class ; biolink:QuantityValue a owl:Class ; rdfs:label "quantity value" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom ; owl:onProperty biolink:has_unit ], [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_numeric_value ], [ a owl:Restriction ; - owl:allValuesFrom ; + owl:minCardinality 0 ; owl:onProperty biolink:has_unit ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:has_numeric_value ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:double ; owl:onProperty biolink:has_numeric_value ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_unit ], biolink:Annotation ; skos:definition "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; @@ -9461,23 +9458,23 @@ biolink:ResourceRoleEnum a owl:Class ; biolink:SequenceFeatureRelationship a owl:Class ; rdfs:label "sequence feature relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:NucleicAcidEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NucleicAcidEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "For example, a particular exon is part of a particular transcript or gene" ; skos:exactMatch CHADO:feature_relationship ; @@ -9596,10 +9593,19 @@ biolink:ClinicalAttribute a owl:Class ; biolink:DatasetVersion a owl:Class ; rdfs:label "dataset version" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:ingest_date ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:ingest_date ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_distribution ], + [ a owl:Restriction ; owl:allValuesFrom biolink:Dataset ; owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:DatasetDistribution ; owl:onProperty biolink:has_distribution ], [ a owl:Restriction ; owl:minCardinality 0 ; @@ -9607,18 +9613,9 @@ biolink:DatasetVersion a owl:Class ; [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:ingest_date ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:ingest_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_dataset ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:ingest_date ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DatasetDistribution ; - owl:onProperty biolink:has_distribution ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_distribution ], @@ -9650,23 +9647,23 @@ biolink:FDAIDAAdverseEventEnum a owl:Class ; biolink:FunctionalAssociation a owl:Class ; rdfs:label "functional association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; skos:inScheme . @@ -10015,6 +10012,14 @@ biolink:stage_qualifier a owl:ObjectProperty ; skos:definition "stage during which gene or protein expression of takes place." ; skos:inScheme . +biolink:subject_of_treatment_application_or_study_for_treatment_by a owl:ObjectProperty ; + rdfs:label "subject of treatment application or study for treatment by" ; + rdfs:domain biolink:ChemicalOrDrugOrTreatment ; + rdfs:range biolink:DiseaseOrPhenotypicFeature ; + rdfs:subPropertyOf biolink:related_to_at_instance_level ; + owl:inverseOf biolink:treats_or_applied_or_studied_to_treat ; + skos:inScheme . + biolink:supporting_study_metadata a owl:DatatypeProperty ; rdfs:label "supporting study metadata" ; rdfs:subPropertyOf biolink:association_slot ; @@ -10047,38 +10052,38 @@ biolink:CellularOrganism a owl:Class ; biolink:ChemicalMixture a owl:Class ; rdfs:label "chemical mixture" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:drug_regulatory_status_world_wide ], - [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:is_supplement ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:highest_FDA_approval_status ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DrugDeliveryEnum ; + owl:onProperty biolink:routes_of_delivery ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:highest_FDA_approval_status ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:drug_regulatory_status_world_wide ], + owl:minCardinality 0 ; + owl:onProperty biolink:routes_of_delivery ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:is_supplement ], + owl:minCardinality 0 ; + owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:highest_FDA_approval_status ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:is_supplement ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DrugDeliveryEnum ; - owl:onProperty biolink:routes_of_delivery ], + owl:maxCardinality 1 ; + owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:is_supplement ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:routes_of_delivery ], biolink:ChemicalEntity ; skos:closeMatch dcid:ChemicalCompound ; skos:definition "A chemical mixture is a chemical entity composed of two or more molecular entities." ; @@ -10104,13 +10109,22 @@ biolink:GeneProductMixin a owl:Class ; biolink:GeneToDiseaseAssociation a owl:Class ; rdfs:label "gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; @@ -10118,15 +10132,6 @@ biolink:GeneToDiseaseAssociation a owl:Class ; [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; skos:closeMatch dcid:DiseaseGeneAssociation ; skos:exactMatch SIO:000983 ; @@ -10144,36 +10149,36 @@ biolink:MolecularActivity a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:enabled_by ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_input ], + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_input ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:Occurrent ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_input ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:enabled_by ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:has_input ], biolink:BiologicalProcessOrActivity ; skos:altLabel "molecular event", "molecular function", @@ -10193,38 +10198,38 @@ biolink:PhysicalEssenceOrOccurrent a owl:Class ; biolink:RetrievalSource a owl:Class ; rdfs:label "retrieval source" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:upstream_resource_ids ], + owl:minCardinality 1 ; + owl:onProperty biolink:resource_role ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:resource_id ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:resource_role ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:resource_id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:upstream_resource_ids ], + owl:allValuesFrom biolink:ResourceRoleEnum ; + owl:onProperty biolink:resource_role ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:resource_role ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:resource_id ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:resource_id ], + owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:xref ], + owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:maxCardinality 1 ; owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:resource_id ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ResourceRoleEnum ; - owl:onProperty biolink:resource_role ], + owl:minCardinality 0 ; + owl:onProperty biolink:xref ], biolink:InformationContentEntity ; skos:definition "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; skos:inScheme . @@ -10594,23 +10599,23 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a owl:Class ; biolink:Genotype a owl:Class ; rdfs:label "genotype" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:Zygosity ; owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Zygosity ; - owl:onProperty biolink:has_zygosity ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_zygosity ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_zygosity ], biolink:BiologicalEntity ; skos:definition "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; skos:exactMatch , @@ -10712,68 +10717,68 @@ biolink:AgentTypeEnum a owl:Class ; biolink:Entity a owl:Class ; rdfs:label "entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:type ], + owl:allValuesFrom biolink:Attribute ; + owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:deprecated ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:type ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:description ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:iri ], + owl:onProperty biolink:deprecated ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:description ], + owl:allValuesFrom biolink:label_type ; + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:allValuesFrom biolink:narrative_text ; owl:onProperty biolink:description ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:deprecated ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:description ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:iri_type ; owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:label_type ; - owl:onProperty biolink:name ], + owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Attribute ; - owl:onProperty biolink:has_attribute ], + owl:onProperty biolink:iri ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:deprecated ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:deprecated ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:category ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:category ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:iri_type ; - owl:onProperty biolink:iri ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:type ], linkml:ClassDefinition ; skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." ; skos:inScheme . @@ -10846,16 +10851,16 @@ biolink:NucleicAcidEntity a owl:Class ; rdfs:label "nucleic acid entity" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ThingWithTaxon ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon ], + owl:someValuesFrom biolink:OntologyClass ], biolink:MolecularEntity ; skos:altLabel "genomic entity", "sequence feature" ; @@ -10871,14 +10876,14 @@ biolink:label_type a rdfs:Datatype ; biolink:OrganismalEntity a owl:Class ; rdfs:label "organismal entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SubjectOfInvestigation ], + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:has_attribute ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SubjectOfInvestigation ], biolink:BiologicalEntity ; skos:definition "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; skos:exactMatch , @@ -10978,37 +10983,37 @@ biolink:GeneOrGeneProductOrChemicalPartQualifierEnum a owl:Class ; biolink:BiologicalProcessOrActivity a owl:Class ; rdfs:label "biological process or activity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:has_output ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:enabled_by ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_input ], + owl:onProperty biolink:has_output ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhysicalEntity ; - owl:onProperty biolink:enabled_by ], + owl:someValuesFrom biolink:Occurrent ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:has_output ], + owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_output ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:PhysicalEntity ; owl:onProperty biolink:enabled_by ], biolink:BiologicalEntity ; skos:definition "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; @@ -11017,38 +11022,38 @@ biolink:BiologicalProcessOrActivity a owl:Class ; biolink:Agent a owl:Class ; rdfs:label "agent" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:address ], + owl:minCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:affiliation ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:address ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], + owl:minCardinality 0 ; + owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:address ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], + owl:maxCardinality 1 ; + owl:onProperty biolink:address ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:affiliation ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:affiliation ], biolink:AdministrativeEntity ; skos:altLabel "group" ; skos:definition "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; @@ -11186,14 +11191,14 @@ biolink:MolecularEntity a owl:Class ; biolink:OrganismTaxon a owl:Class ; rdfs:label "organism taxon" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_taxonomic_rank ], - [ a owl:Restriction ; owl:allValuesFrom biolink:TaxonomicRank ; owl:onProperty biolink:has_taxonomic_rank ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_taxonomic_rank ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_taxonomic_rank ], biolink:NamedThing ; skos:altLabel "taxon", "taxonomic classification" ; @@ -11207,41 +11212,41 @@ biolink:OrganismTaxon a owl:Class ; biolink:InformationContentEntity a owl:Class ; rdfs:label "information content entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:date ; - owl:onProperty biolink:creation_date ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:format ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:rights ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:license ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:license ], + owl:onProperty biolink:rights ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:format ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:license ], + owl:minCardinality 0 ; + owl:onProperty biolink:rights ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:license ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:date ; owl:onProperty biolink:creation_date ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:format ], + owl:maxCardinality 1 ; + owl:onProperty biolink:license ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:format ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:rights ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:rights ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:format ], + owl:onProperty biolink:creation_date ], biolink:NamedThing ; skos:altLabel "information", "information artefact", @@ -11300,50 +11305,50 @@ biolink:CausalMechanismQualifierEnum a owl:Class ; biolink:Attribute a owl:Class ; rdfs:label "attribute" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:has_qualitative_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:has_qualitative_value ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:QuantityValue ; - owl:onProperty biolink:has_quantitative_value ], + owl:allValuesFrom biolink:iri_type ; + owl:onProperty biolink:iri ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_qualitative_value ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; - owl:allValuesFrom biolink:label_type ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:has_attribute_type ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:iri_type ; + owl:maxCardinality 1 ; owl:onProperty biolink:iri ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:has_attribute_type ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:iri ], + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_qualitative_value ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:QuantityValue ; + owl:onProperty biolink:has_quantitative_value ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:iri ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_qualitative_value ], + owl:allValuesFrom biolink:label_type ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], biolink:NamedThing ; skos:definition "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; skos:exactMatch SIO:000614 ; @@ -11355,35 +11360,35 @@ biolink:predicate_type a rdfs:Datatype ; biolink:Gene a owl:Class ; rdfs:label "gene" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:symbol ], + [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:symbol ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:symbol ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneOrGeneProduct ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:symbol ], + owl:minCardinality 0 ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], biolink:BiologicalEntity ; skos:broadMatch ; skos:definition "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; @@ -11397,38 +11402,38 @@ biolink:Gene a owl:Class ; biolink:SequenceVariant a owl:Class ; rdfs:label "sequence variant" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ], + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_gene ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_gene ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:OntologyClass ], biolink:BiologicalEntity ; skos:altLabel "allele" ; skos:closeMatch , @@ -11472,68 +11477,68 @@ biolink:AnatomicalEntity a owl:Class ; biolink:Publication a owl:Class ; rdfs:label "publication" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:keywords ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:pages ], + [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], + owl:onProperty biolink:mesh_terms ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:summary ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:keywords ], + owl:allValuesFrom biolink:Agent ; + owl:onProperty biolink:authors ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:summary ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:pages ], + owl:onProperty biolink:authors ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:minCardinality 0 ; owl:onProperty biolink:mesh_terms ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Agent ; - owl:onProperty biolink:authors ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:summary ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:publication_type ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:authors ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:summary ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:summary ], + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], + owl:onProperty biolink:publication_type ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:pages ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:keywords ], + owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:mesh_terms ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:publication_type ], + owl:onProperty biolink:keywords ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], biolink:InformationContentEntity ; skos:definition "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP)." ; skos:exactMatch IAO:0000311 ; @@ -11566,56 +11571,56 @@ biolink:BiologicalEntity a owl:Class ; biolink:ChemicalEntity a owl:Class ; rdfs:label "chemical entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:is_toxic ], + owl:allValuesFrom biolink:ChemicalRole ; + owl:onProperty biolink:has_chemical_role ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:trade_name ], + owl:allValuesFrom biolink:DrugAvailabilityEnum ; + owl:onProperty biolink:available_from ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DrugAvailabilityEnum ; - owl:onProperty biolink:available_from ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:available_from ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:trade_name ], + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:is_toxic ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:trade_name ], + owl:onProperty biolink:has_chemical_role ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:maxCardinality 1 ; + owl:onProperty biolink:is_toxic ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:max_tolerated_dose ], + owl:onProperty biolink:available_from ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:is_toxic ], + owl:minCardinality 0 ; + owl:onProperty biolink:trade_name ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:is_toxic ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalRole ; - owl:onProperty biolink:has_chemical_role ], + owl:maxCardinality 1 ; + owl:onProperty biolink:trade_name ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], + owl:someValuesFrom biolink:PhysicalEssence ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:trade_name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_chemical_role ], + owl:onProperty biolink:is_toxic ], biolink:NamedThing ; skos:broadMatch STY:T167 ; skos:definition "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; @@ -11750,254 +11755,254 @@ biolink:association_slot a owl:DatatypeProperty ; biolink:Association a owl:Class ; rdfs:label "association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:primary_knowledge_source ], + owl:minCardinality 0 ; + owl:onProperty biolink:category ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:original_predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:original_subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:predicate_type ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_category ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; - owl:onProperty biolink:adjusted_p_value ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_label_closure ], [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:original_predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:p_value ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:retrieval_source_ids ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_category ], + owl:onProperty biolink:subject_label_closure ], [ a owl:Restriction ; - owl:allValuesFrom biolink:RetrievalSource ; - owl:onProperty biolink:retrieval_source_ids ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_label_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:original_object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_label_closure ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; - owl:allValuesFrom biolink:EvidenceType ; - owl:onProperty biolink:has_evidence ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:aggregator_knowledge_source ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:original_subject ], + owl:onProperty biolink:object_category ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:primary_knowledge_source ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:KnowledgeLevelEnum ; + owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:boolean ; owl:onProperty biolink:negated ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_label_closure ], + owl:onProperty biolink:qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_category_closure ], + owl:onProperty biolink:negated ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_category_closure ], + owl:onProperty biolink:object_category ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; + owl:minCardinality 0 ; owl:onProperty biolink:p_value ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:aggregator_knowledge_source ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:subject_category ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:original_object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_evidence ], + owl:onProperty biolink:publications ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_namespace ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:knowledge_level ], + owl:onProperty biolink:original_object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object_category_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualifiers ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AgentTypeEnum ; - owl:onProperty biolink:agent_type ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_closure ], + owl:onProperty biolink:type ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_category_closure ], + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:negated ], + owl:maxCardinality 1 ; + owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_closure ], + owl:minCardinality 1 ; + owl:onProperty biolink:agent_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualifier ], + owl:onProperty biolink:original_object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:subject_category_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_namespace ], + owl:onProperty biolink:aggregator_knowledge_source ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_label_closure ], + owl:onProperty biolink:retrieval_source_ids ], [ a owl:Restriction ; - owl:allValuesFrom biolink:KnowledgeLevelEnum ; - owl:onProperty biolink:knowledge_level ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:float ; + owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:original_object ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:knowledge_source ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_category ], + owl:minCardinality 0 ; + owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:adjusted_p_value ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:category ], + owl:onProperty biolink:subject_closure ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:negated ], + owl:allValuesFrom biolink:time_type ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_namespace ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:qualifiers ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], + owl:onProperty biolink:object_closure ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:primary_knowledge_source ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:original_predicate ], + owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_category ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:original_subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:category ], + owl:allValuesFrom biolink:EvidenceType ; + owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:p_value ], + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:publications ], + owl:onProperty biolink:subject_category_closure ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_category ], + owl:onProperty biolink:qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_label_closure ], + owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:primary_knowledge_source ], + owl:onProperty biolink:object_category ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:aggregator_knowledge_source ], + owl:maxCardinality 1 ; + owl:onProperty biolink:original_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_namespace ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AgentTypeEnum ; + owl:onProperty biolink:agent_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:p_value ], + owl:maxCardinality 1 ; + owl:onProperty biolink:original_subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:float ; + owl:onProperty biolink:p_value ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_closure ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:agent_type ], + owl:minCardinality 0 ; + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_closure ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_category_closure ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:original_subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_closure ], [ a owl:Restriction ; - owl:allValuesFrom biolink:time_type ; - owl:onProperty biolink:timepoint ], + owl:maxCardinality 1 ; + owl:onProperty biolink:qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:agent_type ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:Publication ; owl:onProperty biolink:publications ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:negated ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:knowledge_source ], + owl:onProperty biolink:object_label_closure ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_category_closure ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:original_subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:adjusted_p_value ], + owl:allValuesFrom biolink:RetrievalSource ; + owl:onProperty biolink:retrieval_source_ids ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Entity ; skos:definition "A typed association between two entities, supported by evidence" ; skos:exactMatch OBAN:association, @@ -12017,20 +12022,14 @@ biolink:related_to_at_instance_level a owl:DatatypeProperty, biolink:NamedThing a owl:Class ; rdfs:label "named thing" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:full_name ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:category ], - [ a owl:Restriction ; owl:allValuesFrom biolink:label_type ; owl:onProperty biolink:synonym ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:provided_by ], + owl:allValuesFrom biolink:label_type ; + owl:onProperty biolink:full_name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:synonym ], + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:category ], @@ -12041,14 +12040,20 @@ biolink:NamedThing a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:provided_by ], [ a owl:Restriction ; - owl:allValuesFrom biolink:label_type ; + owl:minCardinality 1 ; + owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:synonym ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:full_name ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:provided_by ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:full_name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:xref ], biolink:Entity ; skos:definition "a databased entity or concept/class" ; skos:exactMatch STY:T071, @@ -12100,108 +12105,84 @@ biolink:subject a owl:ObjectProperty ; skos:inScheme . [] a owl:Restriction ; - rdfs:subClassOf biolink:Mammal ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Mammal . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:biological_sequence ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_biological_sequence ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenomicEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:PosttranslationalModification ; + rdfs:subClassOf biolink:Protein ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PosttranslationalModification . + owl:someValuesFrom biolink:Protein . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathologicalEntityMixin . + rdfs:subClassOf biolink:DatasetSummary ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DatasetSummary . [] a owl:Restriction ; - rdfs:subClassOf biolink:Bacterium ; + rdfs:subClassOf biolink:ClinicalTrial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Bacterium . + owl:someValuesFrom biolink:ClinicalTrial . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom biolink:ExposureEvent ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ] ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FeatureOrDiseaseQualifiersToEntityMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalGeneInteractionAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalGeneInteractionAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToExpressionSiteAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToExpressionSiteAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypicSex ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypicSex . + owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSampleDerivationAssociation ; + rdfs:subClassOf biolink:ComplexMolecularMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSampleDerivationAssociation . + owl:someValuesFrom biolink:ComplexMolecularMixture . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalFeature ; + rdfs:subClassOf biolink:OrganismTaxonToEnvironmentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalFeature . + owl:someValuesFrom biolink:OrganismTaxonToEnvironmentAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty biolink:frequency_qualifier ], + owl:allValuesFrom biolink:CellLine ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -12211,136 +12192,163 @@ biolink:subject a owl:ObjectProperty ; [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:predicate_type ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ] ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQualifierMixin . + owl:someValuesFrom biolink:CellLineToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Snv ; + rdfs:subClassOf biolink:Virus ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Snv . + owl:someValuesFrom biolink:Virus . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceAssociation ; + rdfs:subClassOf biolink:Disease ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceAssociation . + owl:someValuesFrom biolink:Disease . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:PhenotypicQuality ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:PhenotypicQuality . [] a owl:Restriction ; - rdfs:subClassOf biolink:EntityToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:Cohort ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:Cohort . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ClinicalEntity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ClinicalEntity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneAffectsChemicalAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneAffectsChemicalAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:RegulatoryRegion ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:RegulatoryRegion . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneProductIsoformMixin . [] a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:Outcome . [] a owl:Restriction ; - rdfs:subClassOf biolink:SocioeconomicAttribute ; + rdfs:subClassOf biolink:TranscriptionFactorBindingSite ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SocioeconomicAttribute . + owl:someValuesFrom biolink:TranscriptionFactorBindingSite . [] a owl:Restriction ; - rdfs:subClassOf biolink:PairwiseMolecularInteraction ; + rdfs:subClassOf biolink:GeneAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PairwiseMolecularInteraction . + owl:someValuesFrom biolink:GeneAsAModelOfDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:CellLineAsAModelOfDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:CellLineAsAModelOfDiseaseAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene_or_gene_product ], - [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_gene_or_gene_product ] ; + owl:onProperty biolink:timepoint ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:time_type ; + owl:onProperty biolink:timepoint ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:timepoint ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin . + owl:someValuesFrom biolink:ExposureEvent . [] a owl:Restriction ; - rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; + rdfs:subClassOf biolink:VariantAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PopulationOfIndividualOrganisms . + owl:someValuesFrom biolink:VariantAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Device ; + rdfs:subClassOf biolink:BehaviorToBehavioralFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Device . + owl:someValuesFrom biolink:BehaviorToBehavioralFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ComplexChemicalExposure ; + rdfs:subClassOf biolink:CodingSequence ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ComplexChemicalExposure . + owl:someValuesFrom biolink:CodingSequence . [] a owl:Restriction ; - rdfs:subClassOf biolink:Genome ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PairwiseMolecularInteraction ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Genome . + owl:someValuesFrom biolink:PairwiseMolecularInteraction . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinFamily ; + rdfs:subClassOf biolink:GeneToGeneHomologyAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinFamily . + owl:someValuesFrom biolink:GeneToGeneHomologyAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CellLine ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ] ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CellLineToEntityAssociationMixin . + owl:someValuesFrom biolink:ChemicalEntityToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Publication ; + rdfs:subClassOf biolink:CellLine ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Publication . + owl:someValuesFrom biolink:CellLine . [] a owl:Restriction ; - rdfs:subClassOf biolink:Attribute ; + rdfs:subClassOf biolink:Agent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Attribute . + owl:someValuesFrom biolink:Agent . [] a owl:Restriction ; rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; @@ -12348,208 +12356,125 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:DiseaseOrPhenotypicFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:InformationContentEntityToNamedThingAssociation ; + rdfs:subClassOf biolink:FoodAdditive ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:InformationContentEntityToNamedThingAssociation . + owl:someValuesFrom biolink:FoodAdditive . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToMolecularActivityAssociation ; + rdfs:subClassOf biolink:Transcript ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToMolecularActivityAssociation . + owl:someValuesFrom biolink:Transcript . [] a owl:Restriction ; - rdfs:subClassOf biolink:Drug ; + rdfs:subClassOf biolink:BehavioralFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Drug . + owl:someValuesFrom biolink:BehavioralFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetDistribution ; + rdfs:subClassOf biolink:ClinicalCourse ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetDistribution . + owl:someValuesFrom biolink:ClinicalCourse . [] a owl:Restriction ; - rdfs:subClassOf biolink:Polypeptide ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Polypeptide . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SubjectOfInvestigation . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleicAcidEntity ; + rdfs:subClassOf biolink:Procedure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleicAcidEntity . + owl:someValuesFrom biolink:Procedure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalEntity ; + rdfs:subClassOf biolink:Book ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalEntity . + owl:someValuesFrom biolink:Book . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathognomonicityQuantifier . + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonSpecialization ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonSpecialization . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:symbol_type ; - owl:onProperty biolink:name ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineMixin . + rdfs:subClassOf biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EntityToDiseaseAssociation ; + rdfs:subClassOf biolink:EntityToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EntityToDiseaseAssociation . + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExposureEventToOutcomeAssociation ; + rdfs:subClassOf biolink:GeographicLocationAtTime ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExposureEventToOutcomeAssociation . + owl:someValuesFrom biolink:GeographicLocationAtTime . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityToEntityAssociationMixin . + rdfs:subClassOf biolink:SocioeconomicExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:SocioeconomicExposure . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:expression_site ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:phenotypic_state ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:expression_site ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:phenotypic_state ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:expression_site ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:phenotypic_state ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneExpressionMixin . + rdfs:subClassOf biolink:GeneToGoTermAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToGoTermAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalExposure ; + rdfs:subClassOf biolink:PreprintPublication ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalExposure . + owl:someValuesFrom biolink:PreprintPublication . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSample ; + rdfs:subClassOf biolink:SeverityValue ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSample . + owl:someValuesFrom biolink:SeverityValue . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyPopulation ; + rdfs:subClassOf biolink:ProteinFamily ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyPopulation . + owl:someValuesFrom biolink:ProteinFamily . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularComplex ; + rdfs:subClassOf biolink:Onset ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularComplex . + owl:someValuesFrom biolink:Onset . [] a owl:Restriction ; - rdfs:subClassOf biolink:Study ; + rdfs:subClassOf biolink:PathologicalAnatomicalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Study . + owl:someValuesFrom biolink:PathologicalAnatomicalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:RetrievalSource ; + rdfs:subClassOf biolink:TranscriptToGeneRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RetrievalSource . + owl:someValuesFrom biolink:TranscriptToGeneRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonInteraction ; + rdfs:subClassOf biolink:Association ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonInteraction . + owl:someValuesFrom biolink:Association . [] a owl:Restriction ; - rdfs:subClassOf biolink:Cell ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Cell . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:timepoint ], + owl:maxCardinality 1 ; + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; - owl:allValuesFrom biolink:time_type ; - owl:onProperty biolink:timepoint ], + owl:allValuesFrom biolink:biological_sequence ; + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:timepoint ] ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_biological_sequence ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent . + owl:someValuesFrom biolink:EpigenomicEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:JournalArticle ; + rdfs:subClassOf biolink:Mammal ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:JournalArticle . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass . + owl:someValuesFrom biolink:Mammal . [] a owl:Restriction ; rdfs:subClassOf biolink:PopulationToPopulationAssociation ; @@ -12557,39 +12482,43 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:PopulationToPopulationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToVariantAssociation ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToVariantAssociation . + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleosomeModification ; + rdfs:subClassOf biolink:GeneticInheritance ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleosomeModification . + owl:someValuesFrom biolink:GeneticInheritance . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetVersion ; + rdfs:subClassOf biolink:DrugToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetVersion . + owl:someValuesFrom biolink:DrugToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneAssociation ; + rdfs:subClassOf biolink:BehavioralExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneAssociation . + owl:someValuesFrom biolink:BehavioralExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:SeverityValue ; + rdfs:subClassOf biolink:Genome ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SeverityValue . + owl:someValuesFrom biolink:Genome . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleicAcidSequenceMotif ; + rdfs:subClassOf biolink:Serial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleicAcidSequenceMotif . + owl:someValuesFrom biolink:Serial . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:ExposureEventToOutcomeAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:ExposureEventToOutcomeAssociation . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:RelationshipQuantifier . [] a owl:Restriction ; rdfs:subClassOf biolink:GeneToPathwayAssociation ; @@ -12597,339 +12526,278 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:GeneToPathwayAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Exon ; + rdfs:subClassOf biolink:GeographicLocation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Exon . + owl:someValuesFrom biolink:GeographicLocation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalRole ; + rdfs:subClassOf biolink:MolecularActivityToChemicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalRole . + owl:someValuesFrom biolink:MolecularActivityToChemicalEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneProductRelationship ; + rdfs:subClassOf biolink:ChemicalRole ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneProductRelationship . + owl:someValuesFrom biolink:ChemicalRole . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToChemicalEntityAssociation ; + rdfs:subClassOf biolink:MacromolecularMachineToBiologicalProcessAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToChemicalEntityAssociation . + owl:someValuesFrom biolink:MacromolecularMachineToBiologicalProcessAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLineAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:SequenceFeatureRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLineAsAModelOfDiseaseAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation . + owl:someValuesFrom biolink:SequenceFeatureRelationship . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_count ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier . + rdfs:subClassOf biolink:ChemicalEntity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:PreprintPublication ; + rdfs:subClassOf biolink:GeneFamily ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PreprintPublication . + owl:someValuesFrom biolink:GeneFamily . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneOrGeneProduct . + rdfs:subClassOf biolink:PhysicalEntity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PhysicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetSummary ; + rdfs:subClassOf biolink:ChiSquaredAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetSummary . + owl:someValuesFrom biolink:ChiSquaredAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneCoexpressionAssociation ; + rdfs:subClassOf biolink:DruggableGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneCoexpressionAssociation . + owl:someValuesFrom biolink:DruggableGeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToPathwayAssociation ; + rdfs:subClassOf biolink:MolecularActivity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToPathwayAssociation . + owl:someValuesFrom biolink:MolecularActivity . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToMolecularActivityAssociation ; + rdfs:subClassOf biolink:Food ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToMolecularActivityAssociation . + owl:someValuesFrom biolink:Food . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:allValuesFrom biolink:symbol_type ; + owl:onProperty biolink:name ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin . + owl:someValuesFrom biolink:MacromolecularMachineMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:VariantToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:VariantToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin . + rdfs:subClassOf biolink:OrganismalEntityAsAModelOfDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismalEntityAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicLocationAtTime ; + rdfs:subClassOf biolink:OrganismToOrganismAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicLocationAtTime . + owl:someValuesFrom biolink:OrganismToOrganismAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:NamedThing ; + rdfs:subClassOf biolink:Invertebrate ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NamedThing . + owl:someValuesFrom biolink:Invertebrate . [] a owl:Restriction ; - rdfs:subClassOf biolink:EvidenceType ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EvidenceType . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SpecificityQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:Activity ; + rdfs:subClassOf biolink:InformationContentEntityToNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Activity . + owl:someValuesFrom biolink:InformationContentEntityToNamedThingAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:Publication ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:Publication . [] a owl:Restriction ; - rdfs:subClassOf biolink:Invertebrate ; + rdfs:subClassOf biolink:CellularOrganism ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Invertebrate . + owl:someValuesFrom biolink:CellularOrganism . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalFoodContaminant ; + rdfs:subClassOf biolink:TaxonToTaxonAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalFoodContaminant . + owl:someValuesFrom biolink:TaxonToTaxonAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellularComponent ; + rdfs:subClassOf biolink:SequenceAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellularComponent . + owl:someValuesFrom biolink:SequenceAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:VariantToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:VariantToDiseaseAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], + [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin . - -[] a owl:Restriction ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:phenotypic_state ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:stage_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:expression_site ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SensitivityQuantifier . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:PhysicalEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhysicalEntity . + owl:someValuesFrom biolink:GeneExpressionMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToPopulationAssociation ; + rdfs:subClassOf biolink:CausalGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToPopulationAssociation . + owl:someValuesFrom biolink:CausalGeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalProcess ; + rdfs:subClassOf biolink:BiologicalProcessOrActivity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalProcess . + owl:someValuesFrom biolink:BiologicalProcessOrActivity . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReagentTargetedGene ; + rdfs:subClassOf biolink:ClinicalIntervention ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReagentTargetedGene . + owl:someValuesFrom biolink:ClinicalIntervention . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation ; + rdfs:subClassOf biolink:GenomicBackgroundExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . + owl:someValuesFrom biolink:GenomicBackgroundExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:ClinicalFinding ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:ClinicalFinding . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntity . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinIsoform ; + rdfs:subClassOf biolink:Article ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinIsoform . + owl:someValuesFrom biolink:Article . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugToGeneAssociation ; + rdfs:subClassOf biolink:GenomicSequenceLocalization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugToGeneAssociation . + owl:someValuesFrom biolink:GenomicSequenceLocalization . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Outcome ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin . + owl:someValuesFrom biolink:FeatureOrDiseaseQualifiersToEntityMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:TaxonToTaxonAssociation ; + rdfs:subClassOf biolink:MaterialSampleDerivationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TaxonToTaxonAssociation . + owl:someValuesFrom biolink:MaterialSampleDerivationAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:AccessibleDnaRegion ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:AccessibleDnaRegion . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssenceOrOccurrent . [] a owl:Restriction ; rdfs:subClassOf biolink:SequenceVariantModulatesTreatmentAssociation ; @@ -12937,522 +12805,641 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:SequenceVariantModulatesTreatmentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicQuality ; + rdfs:subClassOf biolink:ChemicalMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicQuality . + owl:someValuesFrom biolink:ChemicalMixture . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureExposure ; + rdfs:subClassOf biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureExposure . + owl:someValuesFrom biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CommonDataElement ; + rdfs:subClassOf biolink:GeneToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CommonDataElement . + owl:someValuesFrom biolink:GeneToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:AdministrativeEntity ; + rdfs:subClassOf biolink:ChemicalToChemicalDerivationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AdministrativeEntity . + owl:someValuesFrom biolink:ChemicalToChemicalDerivationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToLocationAssociation ; + rdfs:subClassOf biolink:GenotypeToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . + owl:someValuesFrom biolink:GenotypeToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PlanetaryEntity ; + rdfs:subClassOf biolink:ReactionToCatalystAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PlanetaryEntity . + owl:someValuesFrom biolink:ReactionToCatalystAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Human ; + rdfs:subClassOf biolink:Activity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Human . + owl:someValuesFrom biolink:Activity . [] a owl:Restriction ; - rdfs:subClassOf biolink:Protein ; + rdfs:subClassOf biolink:Bacterium ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Protein . + owl:someValuesFrom biolink:Bacterium . [] a owl:Restriction ; - rdfs:subClassOf biolink:CodingSequence ; + rdfs:subClassOf biolink:NucleicAcidSequenceMotif ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CodingSequence . + owl:someValuesFrom biolink:NucleicAcidSequenceMotif . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin . + owl:someValuesFrom biolink:ActivityAndBehavior . [] a owl:Restriction ; - rdfs:subClassOf biolink:LifeStage ; + rdfs:subClassOf biolink:Snv ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:LifeStage . + owl:someValuesFrom biolink:Snv . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalProcessExposure ; + rdfs:subClassOf biolink:GenotypeToVariantAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalProcessExposure . + owl:someValuesFrom biolink:GenotypeToVariantAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalIntervention ; + rdfs:subClassOf biolink:VariantToPopulationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalIntervention . + owl:someValuesFrom biolink:VariantToPopulationAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:synonym ], [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ] ; + owl:allValuesFrom biolink:label_type ; + owl:onProperty biolink:synonym ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalAnatomicalStructure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalAnatomicalStructure . + owl:someValuesFrom biolink:GeneProductMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToDiseaseAssociation ; + rdfs:subClassOf biolink:StudyResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToDiseaseAssociation . + owl:someValuesFrom biolink:StudyResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToGeneAssociation ; + rdfs:subClassOf biolink:VariantToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToGeneAssociation . + owl:someValuesFrom biolink:VariantToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToGenotypePartAssociation ; + rdfs:subClassOf biolink:GrossAnatomicalStructure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToGenotypePartAssociation . + owl:someValuesFrom biolink:GrossAnatomicalStructure . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToBiologicalProcessAssociation ; + rdfs:subClassOf biolink:GenotypeToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToBiologicalProcessAssociation . + owl:someValuesFrom biolink:GenotypeToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenomicBackgroundExposure ; + rdfs:subClassOf biolink:GenotypeToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenomicBackgroundExposure . + owl:someValuesFrom biolink:GenotypeToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugToGeneInteractionExposure ; + rdfs:subClassOf biolink:Case ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugToGeneInteractionExposure . + owl:someValuesFrom biolink:Case . [] a owl:Restriction ; - rdfs:subClassOf biolink:ComplexMolecularMixture ; + rdfs:subClassOf biolink:DiseaseToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ComplexMolecularMixture . + owl:someValuesFrom biolink:DiseaseToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:SocioeconomicExposure ; + rdfs:subClassOf biolink:BioticExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SocioeconomicExposure . + owl:someValuesFrom biolink:BioticExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneFamily ; + rdfs:subClassOf biolink:GeneToGeneCoexpressionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneFamily . + owl:someValuesFrom biolink:GeneToGeneCoexpressionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MicroRNA ; + rdfs:subClassOf biolink:Fungus ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MicroRNA . + owl:someValuesFrom biolink:Fungus . [] a owl:Restriction ; - rdfs:subClassOf biolink:BookChapter ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BookChapter . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:TranscriptionFactorBindingSite ; + rdfs:subClassOf biolink:DrugLabel ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TranscriptionFactorBindingSite . + owl:someValuesFrom biolink:DrugLabel . [] a owl:Restriction ; - rdfs:subClassOf biolink:SiRNA ; + rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SiRNA . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductIsoformMixin . + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeature ; + rdfs:subClassOf biolink:RelativeFrequencyAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeature . + owl:someValuesFrom biolink:RelativeFrequencyAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:RegulatoryRegion ; + rdfs:subClassOf biolink:NoncodingRNAProduct ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RegulatoryRegion . + owl:someValuesFrom biolink:NoncodingRNAProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:Book ; + rdfs:subClassOf biolink:NucleosomeModification ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Book . + owl:someValuesFrom biolink:NucleosomeModification . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalAttribute ; + rdfs:subClassOf biolink:ProteinDomain ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalAttribute . + owl:someValuesFrom biolink:ProteinDomain . [] a owl:Restriction ; - rdfs:subClassOf biolink:Disease ; + rdfs:subClassOf biolink:GeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Disease . + owl:someValuesFrom biolink:GeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReactionToCatalystAssociation ; + rdfs:subClassOf biolink:EvidenceType ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReactionToCatalystAssociation . + owl:someValuesFrom biolink:EvidenceType . [] a owl:Restriction ; - rdfs:subClassOf biolink:ConfidenceLevel ; + rdfs:subClassOf biolink:SequenceVariant ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ConfidenceLevel . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:synonym ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:label_type ; - owl:onProperty biolink:synonym ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:xref ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductMixin . + owl:someValuesFrom biolink:SequenceVariant . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiagnosticAid ; + rdfs:subClassOf biolink:PhenotypicFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiagnosticAid . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssenceOrOccurrent . + owl:someValuesFrom biolink:PhenotypicFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneticInheritance ; + rdfs:subClassOf biolink:CommonDataElement ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneticInheritance . + owl:someValuesFrom biolink:CommonDataElement . [] a owl:Restriction ; - rdfs:subClassOf biolink:Hospitalization ; + rdfs:subClassOf biolink:BiologicalSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Hospitalization . + owl:someValuesFrom biolink:BiologicalSex . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToGeneAssociation ; + rdfs:subClassOf biolink:NucleicAcidEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToGeneAssociation . + owl:someValuesFrom biolink:NucleicAcidEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:GrossAnatomicalStructure ; + rdfs:subClassOf biolink:AnatomicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GrossAnatomicalStructure . + owl:someValuesFrom biolink:AnatomicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseToExposureEventAssociation ; + rdfs:subClassOf biolink:PlanetaryEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseToExposureEventAssociation . + owl:someValuesFrom biolink:PlanetaryEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismToOrganismAssociation ; + rdfs:subClassOf biolink:PhenotypicSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismToOrganismAssociation . + owl:someValuesFrom biolink:PhenotypicSex . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalModifier ; + rdfs:subClassOf biolink:Cell ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalModifier . + owl:someValuesFrom biolink:Cell . [] a owl:Restriction ; - rdfs:subClassOf biolink:Haplotype ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Haplotype . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:Drug ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:DrugToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToEnvironmentAssociation ; + rdfs:subClassOf biolink:ConfidenceLevel ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToEnvironmentAssociation . + owl:someValuesFrom biolink:ConfidenceLevel . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceFeatureRelationship ; + rdfs:subClassOf biolink:StudyPopulation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceFeatureRelationship . + owl:someValuesFrom biolink:StudyPopulation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToCellularComponentAssociation ; + rdfs:subClassOf biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToCellularComponentAssociation . + owl:someValuesFrom biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneHasVariantThatContributesToDiseaseAssociation ; + rdfs:subClassOf biolink:Exon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneHasVariantThatContributesToDiseaseAssociation . + owl:someValuesFrom biolink:Exon . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivity . + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToPathwayAssociation ; + rdfs:subClassOf biolink:MolecularActivityToPathwayAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToPathwayAssociation . + owl:someValuesFrom biolink:MolecularActivityToPathwayAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicSex ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicSex . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcess ; + rdfs:subClassOf biolink:ChemicalToPathwayAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcess . + owl:someValuesFrom biolink:ChemicalToPathwayAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Fungus ; + rdfs:subClassOf biolink:Study ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Fungus . + owl:someValuesFrom biolink:Study . [] a owl:Restriction ; - rdfs:subClassOf biolink:Entity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Entity . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Case ; + owl:onProperty biolink:subject ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:CaseToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Procedure ; + rdfs:subClassOf biolink:FunctionalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Procedure . + owl:someValuesFrom biolink:FunctionalAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChiSquaredAnalysisResult ; + rdfs:subClassOf biolink:Gene ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChiSquaredAnalysisResult . + owl:someValuesFrom biolink:Gene . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToGeneExpressionAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToGeneExpressionAssociation . + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExposureEventToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:Dataset ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExposureEventToPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct . + owl:someValuesFrom biolink:Dataset . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehavioralFeature ; + rdfs:subClassOf biolink:Hospitalization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehavioralFeature . + owl:someValuesFrom biolink:Hospitalization . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneAffectsChemicalAssociation ; + rdfs:subClassOf biolink:EntityToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneAffectsChemicalAssociation . + owl:someValuesFrom biolink:EntityToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Event ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Event . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Behavior ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Behavior . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Patent ; + rdfs:subClassOf biolink:GenotypeAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Patent . + owl:someValuesFrom biolink:GenotypeAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalMeasurement ; + rdfs:subClassOf biolink:EnvironmentalFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalMeasurement . + owl:someValuesFrom biolink:EnvironmentalFeature . [] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:RelationshipQuantifier . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneHomologyAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneHomologyAssociation . + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalAnatomicalExposure ; + rdfs:subClassOf biolink:DrugToGeneInteractionExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalAnatomicalExposure . + owl:someValuesFrom biolink:DrugToGeneInteractionExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLine ; + rdfs:subClassOf biolink:ChemicalGeneInteractionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLine . + owl:someValuesFrom biolink:ChemicalGeneInteractionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Serial ; + rdfs:subClassOf biolink:DatasetVersion ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Serial . + owl:someValuesFrom biolink:DatasetVersion . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalMixture ; + rdfs:subClassOf biolink:Phenomenon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalMixture . + owl:someValuesFrom biolink:Phenomenon . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation ; + rdfs:subClassOf biolink:ChemicalToChemicalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . + owl:someValuesFrom biolink:ChemicalToChemicalAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CorrelatedGeneToDiseaseAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CorrelatedGeneToDiseaseAssociation . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SensitivityQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:Genotype ; + rdfs:subClassOf biolink:ClinicalAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Genotype . + owl:someValuesFrom biolink:ClinicalAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinDomain ; + rdfs:subClassOf biolink:ContributorAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinDomain . + owl:someValuesFrom biolink:ContributorAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:FunctionalAssociation ; + rdfs:subClassOf biolink:RNAProductIsoform ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:FunctionalAssociation . + owl:someValuesFrom biolink:RNAProductIsoform . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhysiologicalProcess ; + rdfs:subClassOf biolink:OrganismTaxon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhysiologicalProcess . + owl:someValuesFrom biolink:OrganismTaxon . [] a owl:Restriction ; - rdfs:subClassOf biolink:IndividualOrganism ; + rdfs:subClassOf biolink:NamedThing ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:IndividualOrganism . + owl:someValuesFrom biolink:NamedThing . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:Drug ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantAsAModelOfDiseaseAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty biolink:subject ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:biological_sequence ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity . + owl:someValuesFrom biolink:Drug . [] a owl:Restriction ; rdfs:subClassOf biolink:Zygosity ; @@ -13460,575 +13447,528 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:Zygosity . [] a owl:Restriction ; - rdfs:subClassOf biolink:Cohort ; + rdfs:subClassOf biolink:Device ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Cohort . + owl:someValuesFrom biolink:Device . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcessOrActivity ; + rdfs:subClassOf biolink:DiagnosticAid ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcessOrActivity . + owl:someValuesFrom biolink:DiagnosticAid . [] a owl:Restriction ; - rdfs:subClassOf biolink:Vertebrate ; + rdfs:subClassOf biolink:Pathway ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Vertebrate . + owl:someValuesFrom biolink:Pathway . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceVariant ; + rdfs:subClassOf biolink:Polypeptide ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceVariant . + owl:someValuesFrom biolink:Polypeptide . [] a owl:Restriction ; - rdfs:subClassOf biolink:AccessibleDnaRegion ; + rdfs:subClassOf biolink:WebPage ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AccessibleDnaRegion . + owl:someValuesFrom biolink:WebPage . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin . + rdfs:subClassOf biolink:OrganismAttribute ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:FoodAdditive ; + rdfs:subClassOf biolink:GenotypeToGenotypePartAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:FoodAdditive . + owl:someValuesFrom biolink:GenotypeToGenotypePartAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonSpecialization ; + rdfs:subClassOf biolink:Treatment ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonSpecialization . + owl:someValuesFrom biolink:Treatment . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin . + rdfs:subClassOf biolink:Behavior ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Behavior . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToChemicalDerivationAssociation ; + rdfs:subClassOf biolink:ClinicalModifier ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToChemicalDerivationAssociation . + owl:someValuesFrom biolink:ClinicalModifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:BioticExposure ; + rdfs:subClassOf biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BioticExposure . + owl:someValuesFrom biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:biological_sequence ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EpigenomicEntity . + rdfs:subClassOf biolink:GeographicExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeographicExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation ; + rdfs:subClassOf biolink:PathologicalProcessExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . + owl:someValuesFrom biolink:PathologicalProcessExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalAffectsGeneAssociation ; + rdfs:subClassOf biolink:DrugExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalAffectsGeneAssociation . + owl:someValuesFrom biolink:DrugExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismalEntity ; + rdfs:subClassOf biolink:ReagentTargetedGene ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismalEntity . + owl:someValuesFrom biolink:ReagentTargetedGene . [] a owl:Restriction ; - rdfs:subClassOf biolink:Plant ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Plant . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Dataset ; + rdfs:subClassOf biolink:ChemicalAffectsGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Dataset . + owl:someValuesFrom biolink:ChemicalAffectsGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProcessedMaterial ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProcessedMaterial . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PathognomonicityQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalTrial ; + rdfs:subClassOf biolink:MolecularMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalTrial . + owl:someValuesFrom biolink:MolecularMixture . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:predicate_type ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MaterialSample ; - owl:onProperty biolink:subject ] ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin . + owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityAssessesNamedThingAssociation ; + rdfs:subClassOf biolink:EnvironmentalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityAssessesNamedThingAssociation . + owl:someValuesFrom biolink:EnvironmentalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ObservedExpectedFrequencyAnalysisResult ; + rdfs:subClassOf biolink:Entity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ObservedExpectedFrequencyAnalysisResult . + owl:someValuesFrom biolink:Entity . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:EnvironmentalFoodContaminant ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:EnvironmentalFoodContaminant . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismAttribute ; + rdfs:subClassOf biolink:BiologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismAttribute . + owl:someValuesFrom biolink:BiologicalProcess . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:in_taxon_label ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:in_taxon ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:in_taxon_label ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:in_taxon ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:label_type ; - owl:onProperty biolink:in_taxon_label ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:in_taxon ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon . + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Food ; + rdfs:subClassOf biolink:ProcessedMaterial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Food . + owl:someValuesFrom biolink:ProcessedMaterial . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGoTermAssociation ; + rdfs:subClassOf biolink:Event ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGoTermAssociation . + owl:someValuesFrom biolink:Event . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToDiseaseAssociation ; + rdfs:subClassOf biolink:CellularComponent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToDiseaseAssociation . + owl:someValuesFrom biolink:CellularComponent . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalFinding ; + rdfs:subClassOf biolink:MaterialSample ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalFinding . + owl:someValuesFrom biolink:MaterialSample . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SubjectOfInvestigation . + rdfs:subClassOf biolink:GeneToGeneFamilyAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToGeneFamilyAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicLocation ; + rdfs:subClassOf biolink:CorrelatedGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicLocation . + owl:someValuesFrom biolink:CorrelatedGeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Pathway ; + rdfs:subClassOf biolink:BiologicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Pathway . + owl:someValuesFrom biolink:BiologicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:TranscriptToGeneRelationship ; + rdfs:subClassOf biolink:OrganismalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TranscriptToGeneRelationship . + owl:someValuesFrom biolink:OrganismalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:Onset ; + rdfs:subClassOf biolink:ChemicalEntityAssessesNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Onset . + owl:someValuesFrom biolink:ChemicalEntityAssessesNamedThingAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxon ; + rdfs:subClassOf biolink:GeneHasVariantThatContributesToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxon . + owl:someValuesFrom biolink:GeneHasVariantThatContributesToDiseaseAssociation . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment . + rdfs:subClassOf biolink:StudyVariable ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:StudyVariable . [] a owl:Restriction ; - rdfs:subClassOf biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation ; + rdfs:subClassOf biolink:SocioeconomicAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . + owl:someValuesFrom biolink:SocioeconomicAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehaviorToBehavioralFeatureAssociation ; + rdfs:subClassOf biolink:ComplexChemicalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehaviorToBehavioralFeatureAssociation . + owl:someValuesFrom biolink:ComplexChemicalExposure . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide . + rdfs:subClassOf biolink:ConceptCountAnalysisResult ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ConceptCountAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugExposure ; + rdfs:subClassOf biolink:MacromolecularMachineToCellularComponentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugExposure . + owl:someValuesFrom biolink:MacromolecularMachineToCellularComponentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugLabel ; + rdfs:subClassOf biolink:MolecularActivityToMolecularActivityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugLabel . + owl:someValuesFrom biolink:MolecularActivityToMolecularActivityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToChemicalAssociation ; + rdfs:subClassOf biolink:SiRNA ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToChemicalAssociation . + owl:someValuesFrom biolink:SiRNA . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:PopulationOfIndividualOrganisms . [] a owl:Restriction ; - rdfs:subClassOf biolink:PairwiseGeneToGeneInteraction ; + rdfs:subClassOf biolink:RetrievalSource ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PairwiseGeneToGeneInteraction . + owl:someValuesFrom biolink:RetrievalSource . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismalEntityAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:LogOddsAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismalEntityAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:LogOddsAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:Case ; + rdfs:subClassOf biolink:DiseaseToExposureEventAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Case . + owl:someValuesFrom biolink:DiseaseToExposureEventAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:MacromolecularMachineToMolecularActivityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:MacromolecularMachineToMolecularActivityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneOrGeneProduct . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PathologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityAssociation . + owl:someValuesFrom biolink:PathologicalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeatureToDiseaseAssociation ; + rdfs:subClassOf biolink:Attribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeatureToDiseaseAssociation . + owl:someValuesFrom biolink:Attribute . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence . + rdfs:subClassOf biolink:Plant ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Plant . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PairwiseGeneToGeneInteraction ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PairwiseGeneToGeneInteraction . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Outcome ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:predicate_type ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ExposureEvent ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin . + owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:NoncodingRNAProduct ; + rdfs:subClassOf biolink:MacromolecularComplex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NoncodingRNAProduct . + owl:someValuesFrom biolink:MacromolecularComplex . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneFamilyAssociation ; + rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneFamilyAssociation . + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyVariable ; + rdfs:subClassOf biolink:SmallMolecule ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyVariable . + owl:someValuesFrom biolink:SmallMolecule . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalCourse ; + rdfs:subClassOf biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalCourse . + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; + rdfs:subClassOf biolink:GeneToGeneProductRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonAssociation . + owl:someValuesFrom biolink:GeneToGeneProductRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:BookChapter ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:BookChapter . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToLocationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Virus ; + rdfs:subClassOf biolink:Patent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Virus . + owl:someValuesFrom biolink:Patent . [] a owl:Restriction ; - rdfs:subClassOf biolink:DruggableGeneToDiseaseAssociation ; + rdfs:subClassOf biolink:PhysiologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DruggableGeneToDiseaseAssociation . + owl:someValuesFrom biolink:PhysiologicalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:CausalGeneToDiseaseAssociation ; + rdfs:subClassOf biolink:Vertebrate ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CausalGeneToDiseaseAssociation . + owl:someValuesFrom biolink:Vertebrate . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalProcess ; + rdfs:subClassOf biolink:GenotypicSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalProcess . + owl:someValuesFrom biolink:GenotypicSex . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalEntity ; + rdfs:subClassOf biolink:ClinicalMeasurement ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalEntity . + owl:someValuesFrom biolink:ClinicalMeasurement . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToDiseaseAssociation ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:Occurrent . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonInteraction ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToDiseaseAssociation . + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonInteraction . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SpecificityQuantifier . + rdfs:subClassOf biolink:Haplotype ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Haplotype . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PhenotypicFeatureToDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PhenotypicFeatureToDiseaseAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:double ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Drug ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DrugToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:InformationContentEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:InformationContentEntity . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:sex_qualifier ], + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:sex_qualifier ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ] ; + owl:allValuesFrom xsd:double ; + owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_count ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin . + owl:someValuesFrom biolink:FrequencyQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:Treatment ; + rdfs:subClassOf biolink:Genotype ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Treatment . + owl:someValuesFrom biolink:Genotype . [] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:id ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ActivityAndBehavior . + owl:someValuesFrom biolink:OntologyClass . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalSex ; + rdfs:subClassOf biolink:LifeStage ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalSex . + owl:someValuesFrom biolink:LifeStage . [] a owl:Restriction ; - rdfs:subClassOf biolink:Agent ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Agent . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenomicSequenceLocalization ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenomicSequenceLocalization . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin . [] a owl:Restriction ; rdfs:subClassOf biolink:TextMiningResult ; @@ -14036,167 +13976,194 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:TextMiningResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularMixture ; + rdfs:subClassOf biolink:PathologicalAnatomicalStructure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularMixture . + owl:someValuesFrom biolink:PathologicalAnatomicalStructure . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent . + rdfs:subClassOf biolink:RNAProduct ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:RNAProduct . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FrequencyQualifierMixin . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ] ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin . + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ContributorAssociation ; + rdfs:subClassOf biolink:PosttranslationalModification ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ContributorAssociation . + owl:someValuesFrom biolink:PosttranslationalModification . [] a owl:Restriction ; - rdfs:subClassOf biolink:WebPage ; + rdfs:subClassOf biolink:EnvironmentalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:WebPage . + owl:someValuesFrom biolink:EnvironmentalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:Transcript ; + rdfs:subClassOf biolink:IndividualOrganism ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Transcript . + owl:someValuesFrom biolink:IndividualOrganism . [] a owl:Restriction ; - rdfs:subClassOf biolink:RNAProductIsoform ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RNAProductIsoform . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:in_taxon_label ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:in_taxon_label ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:label_type ; + owl:onProperty biolink:in_taxon_label ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ThingWithTaxon . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicExposure ; + rdfs:subClassOf biolink:ExposureEventToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicExposure . + owl:someValuesFrom biolink:ExposureEventToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:SmallMolecule ; + rdfs:subClassOf biolink:ExonToTranscriptRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SmallMolecule . + owl:someValuesFrom biolink:ExonToTranscriptRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:CaseToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:GeneToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CaseToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:GeneToPhenotypicFeatureAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhenotypicFeature ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:predicate_type ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalExposure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ReactionToParticipantAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReactionToParticipantAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:CellularOrganism ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellularOrganism . + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:RNAProduct ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RNAProduct . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_gene_or_gene_product ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene_or_gene_product ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneGroupingMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Gene ; + rdfs:subClassOf biolink:Human ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Gene . + owl:someValuesFrom biolink:Human . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], @@ -14205,105 +14172,143 @@ biolink:subject a owl:ObjectProperty ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Case ; - owl:onProperty biolink:subject ] ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CaseToEntityAssociationMixin . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntity ; + rdfs:subClassOf biolink:JournalArticle ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntity . + owl:someValuesFrom biolink:JournalArticle . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneToExpressionSiteAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToExpressionSiteAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:predicate_type ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Genotype ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin . + owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:RelativeFrequencyAnalysisResult ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PathologicalEntityMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DatasetDistribution ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RelativeFrequencyAnalysisResult . + owl:someValuesFrom biolink:DatasetDistribution . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehavioralExposure ; + rdfs:subClassOf biolink:ObservedExpectedFrequencyAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehavioralExposure . + owl:someValuesFrom biolink:ObservedExpectedFrequencyAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:Article ; + rdfs:subClassOf biolink:ChemicalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Article . + owl:someValuesFrom biolink:ChemicalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyResult ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ReactionToParticipantAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyResult . + owl:someValuesFrom biolink:ReactionToParticipantAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:predicate_type ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MaterialSample ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:AdministrativeEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:AdministrativeEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:Association ; + rdfs:subClassOf biolink:MolecularEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Association . + owl:someValuesFrom biolink:MolecularEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:ConceptCountAnalysisResult ; + rdfs:subClassOf biolink:ProteinIsoform ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ConceptCountAnalysisResult . + owl:someValuesFrom biolink:ProteinIsoform . [] a owl:Restriction ; - rdfs:subClassOf biolink:Phenomenon ; + rdfs:subClassOf biolink:MicroRNA ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Phenomenon . + owl:someValuesFrom biolink:MicroRNA . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularEntity ; + rdfs:subClassOf biolink:CaseToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularEntity . + owl:someValuesFrom biolink:CaseToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:LogOddsAnalysisResult ; + rdfs:subClassOf biolink:VariantToGeneExpressionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:LogOddsAnalysisResult . + owl:someValuesFrom biolink:VariantToGeneExpressionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExonToTranscriptRelationship ; + rdfs:subClassOf biolink:InformationContentEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExonToTranscriptRelationship . + owl:someValuesFrom biolink:InformationContentEntity . diff --git a/project/shacl/biolink_model.shacl.ttl b/project/shacl/biolink_model.shacl.ttl index f23b71769..5c601d247 100644 --- a/project/shacl/biolink_model.shacl.ttl +++ b/project/shacl/biolink_model.shacl.ttl @@ -18,115 +18,115 @@ biolink:AccessibleDnaRegion a sh:NodeShape ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 8 ; + sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ] ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:AccessibleDnaRegion . biolink:Activity a sh:NodeShape ; sh:closed true ; sh:description "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ] ; + sh:order 9 ; + sh:path dct:description ] ; sh:targetClass biolink:Activity . biolink:ActivityAndBehavior a sh:NodeShape ; @@ -138,51 +138,51 @@ biolink:ActivityAndBehavior a sh:NodeShape ; biolink:AdministrativeEntity a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:deprecated ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 3 ; sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 2 ; @@ -192,168 +192,105 @@ biolink:AdministrativeEntity a sh:NodeShape ; biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 30 ; sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], [ sh:class biolink:AnatomicalEntity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -365,143 +302,200 @@ biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ] ; - sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityAssociation . - -biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:description "a point in time" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ] ; + sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityAssociation . + +biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; sh:path biolink:object_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at a later time" ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 35 ; sh:path dct:description ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -509,82 +503,48 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at an earlier time" ; + sh:description "the structure at a later time" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the structure at an earlier time" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ] ; - sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . - -biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; @@ -593,48 +553,53 @@ biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the part" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; - sh:path biolink:p_value ], + sh:path biolink:p_value ] ; + sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . + +biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -642,6 +607,20 @@ biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:AnatomicalEntity ; sh:description "the whole" ; sh:maxCount 1 ; @@ -649,125 +628,146 @@ biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the part" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ] ; + sh:order 35 ; + sh:path dct:description ] ; sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . biolink:Annotation a sh:NodeShape ; @@ -780,219 +780,215 @@ biolink:Article a sh:NodeShape ; sh:closed true ; sh:description "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 10 ; - sh:path dct:type ], - [ sh:description "mesh terms tagging a publication" ; + sh:property [ sh:description "mesh terms tagging a publication" ; sh:order 8 ; sh:path biolink:mesh_terms ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:format ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 18 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 20 ; - sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:iso_abbreviation ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 15 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:creation_date ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 20 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:summary ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 7 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 5 ; - sh:path biolink:pages ], + sh:order 21 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:issue ], - [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 9 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:volume ], + sh:order 19 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path dct:description ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 17 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:license ], - [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; + [ sh:datatype xsd:string ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:published_in ], + sh:order 2 ; + sh:path biolink:volume ], [ sh:datatype xsd:string ; - sh:order 21 ; - sh:path rdf:type ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 15 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 5 ; + sh:path biolink:pages ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:authors ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 17 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 9 ; - sh:path biolink:xref ], + sh:order 24 ; + sh:path biolink:has_attribute ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:order 10 ; + sh:path dct:type ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:format ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:authors ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:order 25 ; - sh:path biolink:deprecated ] ; + sh:path biolink:deprecated ], + [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:published_in ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:order 7 ; + sh:path biolink:keywords ] ; sh:targetClass biolink:Article . biolink:Association a sh:NodeShape ; sh:closed true ; sh:description "A typed association between two entities, supported by evidence" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; @@ -1003,13 +999,11 @@ biolink:Association a sh:NodeShape ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -1017,174 +1011,219 @@ biolink:Association a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 35 ; + sh:path dct:description ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:description "a point in time" ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ] ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ] ; sh:targetClass biolink:Association . biolink:Bacterium a sh:NodeShape ; sh:closed true ; sh:description "A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ] ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:Bacterium . biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 33 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Behavior ; sh:description "behavior that is the subject of the association" ; sh:maxCount 1 ; @@ -1192,65 +1231,41 @@ biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], + sh:order 44 ; + sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:has_total ], + sh:order 47 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + sh:order 43 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 45 ; + sh:path biolink:object_aspect_qualifier ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -1258,34 +1273,58 @@ biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:knowledge_level ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 35 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_direction_qualifier ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:class biolink:BehavioralFeature ; sh:description "behavioral feature that is the object of the association" ; sh:maxCount 1 ; @@ -1293,127 +1332,103 @@ biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:description "a human-readable description of an entity" ; + sh:order 41 ; + sh:path biolink:has_quotient ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:order 46 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 17 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:negated ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:order 40 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ] ; + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ] ; sh:targetClass biolink:BehaviorToBehavioralFeatureAssociation . biolink:BehavioralExposure a sh:NodeShape ; sh:closed true ; sh:description "A behavioral exposure is a factor relating to behavior impacting an individual." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:order 12 ; sh:path rdf:type ], @@ -1423,10 +1438,32 @@ biolink:BehavioralExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:description "a point in time" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 13 ; + sh:path dct:description ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 1 ; @@ -1437,83 +1474,55 @@ biolink:BehavioralExposure a sh:NodeShape ; [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], + sh:path biolink:full_name ] ; + sh:targetClass biolink:BehavioralExposure . + +biolink:BehavioralOutcome a sh:NodeShape ; + sh:closed true ; + sh:description "An outcome resulting from an exposure event which is the manifestation of human behavior." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:BehavioralOutcome . + +biolink:BiologicalEntity a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; sh:order 11 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ] ; - sh:targetClass biolink:BehavioralExposure . - -biolink:BehavioralOutcome a sh:NodeShape ; - sh:closed true ; - sh:description "An outcome resulting from an exposure event which is the manifestation of human behavior." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:BehavioralOutcome . - -biolink:BiologicalEntity a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; @@ -1521,47 +1530,38 @@ biolink:BiologicalEntity a sh:NodeShape ; [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:BiologicalEntity . biolink:BiologicalProcessOrActivity a sh:NodeShape ; sh:closed true ; sh:description "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 0 ; + sh:path biolink:has_input ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path dct:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -1572,20 +1572,9 @@ biolink:BiologicalProcessOrActivity a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_output ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_input ], + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -1595,149 +1584,155 @@ biolink:BiologicalProcessOrActivity a sh:NodeShape ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:iri ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:enabled_by ], [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_output ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:enabled_by ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:in_taxon_label ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ] ; + sh:order 13 ; + sh:path rdfs:label ] ; sh:targetClass biolink:BiologicalProcessOrActivity . biolink:BioticExposure a sh:NodeShape ; sh:closed true ; sh:description "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 1 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:description "a point in time" ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 9 ; + sh:path biolink:full_name ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 10 ; sh:path biolink:synonym ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:class biolink:NamedThing ; + [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], + sh:order 2 ; + sh:path biolink:has_attribute_type ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 8 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:BioticExposure . - -biolink:Book a sh:NodeShape ; - sh:closed true ; - sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:path biolink:xref ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:rights ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:deprecated ], + sh:order 5 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:BioticExposure . + +biolink:Book a sh:NodeShape ; + sh:closed true ; + sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "Should generally be set to an ontology class defined term for 'book'." ; + sh:order 17 ; + sh:path rdf:type ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 16 ; sh:path biolink:category ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "Books should have industry-standard identifier such as from ISBN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 6 ; - sh:path dct:type ], + sh:order 8 ; + sh:path biolink:rights ], [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:order 18 ; @@ -1748,66 +1743,84 @@ biolink:Book a sh:NodeShape ; sh:order 10 ; sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "Should generally be set to an ontology class defined term for 'book'." ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:order 6 ; + sh:path dct:type ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:summary ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 11 ; sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ] ; + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:description "Books should have industry-standard identifier such as from ISBN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:format ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path dct:description ] ; sh:targetClass biolink:Book . biolink:BookChapter a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:property [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path rdfs:label ], + sh:order 5 ; + sh:path biolink:summary ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 4 ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:order 20 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; sh:order 6 ; @@ -1816,101 +1829,88 @@ biolink:BookChapter a sh:NodeShape ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:license ], + sh:order 22 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:summary ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 4 ; - sh:path biolink:pages ], + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:id ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 16 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 14 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:creation_date ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:authors ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:license ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:order 9 ; sh:path dct:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:volume ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:creation_date ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 7 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - sh:order 20 ; - sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:rights ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], + sh:order 18 ; + sh:path biolink:iri ], [ sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; sh:path biolink:published_in ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "chapter of a book" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:chapter ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 14 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:deprecated ] ; + [ sh:description "mesh terms tagging a publication" ; + sh:order 7 ; + sh:path biolink:mesh_terms ] ; sh:targetClass biolink:BookChapter . biolink:CaseToEntityAssociationMixin a sh:NodeShape ; @@ -1942,46 +1942,153 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 44 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Case ; + sh:description "the case (e.g. patient) that has the property" ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:subject_aspect_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:order 42 ; sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:has_quotient ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; @@ -1992,6 +2099,16 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_object ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -1999,397 +2116,255 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "a point in time" ; sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:has_count ], + sh:order 47 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 27 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:has_count ] ; + sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . + +biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:order 47 ; sh:path biolink:qualified_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:order 6 ; - sh:path biolink:qualifiers ], + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 17 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:order 26 ; + sh:path biolink:subject_namespace ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; sh:order 35 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 23 ; + sh:order 25 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Case ; - sh:description "the case (e.g. patient) that has the property" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_quotient ] ; - sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . - -biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], + sh:order 38 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], + sh:order 44 ; + sh:path biolink:has_percentage ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:sex_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:has_count ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], + sh:order 24 ; + sh:path biolink:subject_category_closure ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 18 ; sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_percentage ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], + sh:order 33 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 27 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:order 42 ; + sh:path biolink:has_total ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 37 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 34 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_count ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a human-readable description of an entity" ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ], + sh:order 19 ; + sh:path biolink:original_object ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "gene in which variation is shown to cause the disease." ; sh:maxCount 1 ; @@ -2398,133 +2373,169 @@ biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], + sh:order 43 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 40 ; sh:path biolink:deprecated ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ] ; + sh:order 14 ; + sh:path biolink:knowledge_level ] ; sh:targetClass biolink:CausalGeneToDiseaseAssociation . biolink:Cell a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Cell . biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 38 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:CellLine ; + sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; @@ -2535,44 +2546,42 @@ biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 33 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:qualified_predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:object_aspect_qualifier ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:class biolink:CellLine ; - sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -2580,275 +2589,242 @@ biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 42 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:description "The relationship to the disease" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 39 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ] ; - sh:targetClass biolink:CellLineAsAModelOfDiseaseAssociation . - -biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 35 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 40 ; + sh:path biolink:object_aspect_qualifier ] ; + sh:targetClass biolink:CellLineAsAModelOfDiseaseAssociation . + +biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -2856,60 +2832,84 @@ biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ] ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; @@ -2923,18 +2923,18 @@ biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ] ; + sh:path rdf:object ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:CellLineToEntityAssociationMixin . biolink:CellularOrganism a sh:NodeShape ; @@ -2945,17 +2945,35 @@ biolink:CellularOrganism a sh:NodeShape ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; @@ -2964,20 +2982,15 @@ biolink:CellularOrganism a sh:NodeShape ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], @@ -2985,20 +2998,7 @@ biolink:CellularOrganism a sh:NodeShape ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:CellularOrganism . biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; @@ -3006,36 +3006,76 @@ biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; sh:description "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:object_context_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:subject_context_qualifier ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:timepoint ], + sh:order 44 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 39 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 52 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 47 ; - sh:path biolink:category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 29 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:qualified_predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; - sh:path rdf:predicate ], + sh:order 26 ; + sh:path biolink:knowledge_level ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:timepoint ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:causal_mechanism_qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 25 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 35 ; + sh:path biolink:object_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -3043,192 +3083,180 @@ biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 27 ; sh:path biolink:agent_type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:order 33 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:qualifiers ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + sh:in ( "metabolite" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 45 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 14 ; + sh:path biolink:species_context_qualifier ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:original_predicate ], + sh:order 50 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:object_part_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 34 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:knowledge_source ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:order 38 ; + sh:path biolink:subject_namespace ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:causal_mechanism_qualifier ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:order 30 ; + sh:path biolink:original_predicate ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:order 46 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_form_or_variant_qualifier ], + sh:order 43 ; + sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:subject_category ], - [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; - sh:in ( "metabolite" ) ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 51 ; - sh:path biolink:has_attribute ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 17 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:object_category ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 48 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 19 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:subject_category_closure ], + sh:order 18 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 41 ; sh:path biolink:object_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 34 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 51 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 49 ; - sh:path rdfs:label ], + sh:order 52 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 25 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:subject_part_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:iri ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 17 ; - sh:path rdf:object ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 50 ; - sh:path dct:description ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:object_context_qualifier ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:species_context_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 40 ; sh:path biolink:subject_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:publications ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 48 ; + sh:path rdf:type ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 16 ; + sh:path rdf:predicate ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:p_value ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 49 ; + sh:path rdfs:label ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 47 ; + sh:path biolink:category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:adjusted_p_value ], + sh:order 5 ; + sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:ChemicalEntity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -3237,97 +3265,33 @@ biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; sh:order 15 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 35 ; - sh:path biolink:object_closure ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:publications ] ; + sh:minCount 1 ; + sh:order 45 ; + sh:path biolink:id ] ; sh:targetClass biolink:ChemicalAffectsGeneAssociation . biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -3335,104 +3299,104 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:description "a point in time" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:class biolink:ChemicalEntity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -3440,53 +3404,82 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "a human-readable description of an entity" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ] ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ] ; sh:targetClass biolink:ChemicalEntityAssessesNamedThingAssociation . biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "A regulatory relationship between two genes" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 0 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; @@ -3496,52 +3489,52 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 31 ; sh:path biolink:id ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "the direction is always from regulator to regulated" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -3549,119 +3542,126 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape sh:minCount 1 ; sh:order 12 ; sh:path biolink:knowledge_level ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 30 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path rdf:object ], + sh:order 1 ; + sh:path rdf:subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 32 ; sh:path biolink:iri ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 17 ; sh:path biolink:original_object ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; - sh:path biolink:object_category ], - [ sh:description "the direction is always from regulator to regulated" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ] ; + sh:path biolink:object_category ] ; sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . biolink:ChemicalEntityOrProteinOrPolypeptide a sh:NodeShape ; @@ -3699,30 +3699,21 @@ biolink:ChemicalExposure a sh:NodeShape ; sh:closed true ; sh:description "A chemical exposure is an intake of a particular chemical entity." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -3730,164 +3721,87 @@ biolink:ChemicalExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_attribute_type ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path biolink:has_quantitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ] ; - sh:targetClass biolink:ChemicalExposure . - -biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:subject_closure ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:subject_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 1 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 20 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 33 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:GeneOrGeneProduct ; + sh:order 15 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:ChemicalExposure . + +biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:GeneOrGeneProduct ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 10 ; sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_source ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:object_part_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 44 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:p_value ], + sh:order 13 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 34 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 18 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 5 ; + sh:path biolink:object_part_qualifier ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; @@ -3898,42 +3812,67 @@ biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 9 ; sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:qualifiers ], + sh:order 26 ; + sh:path biolink:object_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:object_namespace ], + sh:order 16 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 33 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path rdf:subject ], [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:object_context_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:subject_context_qualifier ], - [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; - sh:in ( "metabolite" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], + sh:order 29 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 41 ; + sh:path rdf:type ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 38 ; - sh:path biolink:id ], + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:publications ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 44 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -3942,167 +3881,228 @@ biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 40 ; sh:path biolink:category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:timepoint ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path dct:description ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:order 32 ; + sh:path biolink:object_namespace ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 41 ; - sh:path rdf:type ], + sh:order 23 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical entity or entity that is an interactor" ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:subject ], + sh:order 7 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 34 ; + sh:path biolink:object_label_closure ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 39 ; sh:path biolink:iri ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:minCount 1 ; + sh:order 20 ; + sh:path biolink:agent_type ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 38 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:publications ], + sh:order 30 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:subject_context_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:p_value ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 17 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:original_predicate ] ; + sh:order 42 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:subject_namespace ], + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + sh:in ( "metabolite" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:timepoint ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 18 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ] ; sh:targetClass biolink:ChemicalGeneInteractionAssociation . biolink:ChemicalMixture a sh:NodeShape ; sh:closed true ; sh:description "A chemical mixture is a chemical entity composed of two or more molecular entities." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:id ], + sh:order 15 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 12 ; - sh:path biolink:synonym ], + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], + sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_chemical_role ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], + sh:order 17 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:order 16 ; + sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 18 ; sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:is_toxic ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 12 ; + sh:path biolink:synonym ], [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; sh:order 3 ; sh:path biolink:routes_of_delivery ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], [ sh:datatype xsd:string ; - sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:description "a long-form human readable name for a thing" ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ] ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ] ; sh:targetClass biolink:ChemicalMixture . biolink:ChemicalOrDrugOrTreatment a sh:NodeShape ; @@ -4115,150 +4115,116 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category_closure ], - [ sh:description "" ; - sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:FDA_adverse_event_level ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 11 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:category ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 35 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:qualifiers ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 31 ; + sh:path biolink:id ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -4266,181 +4232,207 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:minCount 1 ; sh:order 13 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 17 ; sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ] ; - sh:targetClass biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . - -biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:description "" ; + sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 3 ; + sh:path biolink:FDA_adverse_event_level ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path dct:description ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:timepoint ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 21 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; + sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ] ; + sh:targetClass biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . + +biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 27 ; sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; @@ -4449,13 +4441,10 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:No sh:order 3 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a human-readable description of an entity" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -4463,216 +4452,152 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:No sh:minCount 1 ; sh:order 13 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], [ sh:description "" ; sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:FDA_adverse_event_level ] ; - sh:targetClass biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . - -biolink:ChemicalToChemicalAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:path biolink:FDA_adverse_event_level ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; + sh:order 2 ; sh:path rdf:predicate ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:category ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:order 12 ; - sh:path biolink:agent_type ], + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; + sh:order 21 ; sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical element that is the target of the statement" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path biolink:has_evidence ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 32 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . + +biolink:ChemicalToChemicalAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; @@ -4680,174 +4605,268 @@ biolink:ChemicalToChemicalAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ] ; - sh:targetClass biolink:ChemicalToChemicalAssociation . - -biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the upstream chemical entity" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 32 ; - sh:path biolink:iri ], + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; + sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:ChemicalEntity ; - sh:description "the downstream chemical entity" ; + sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; + sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path biolink:catalyst_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:ChemicalToChemicalAssociation . + +biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], + sh:order 7 ; + sh:path biolink:publications ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the downstream chemical entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 25 ; sh:path biolink:object_namespace ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the upstream chemical entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path biolink:catalyst_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 36 ; @@ -4856,19 +4875,16 @@ biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 27 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_object ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -4876,29 +4892,13 @@ biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ] ; + sh:order 12 ; + sh:path biolink:knowledge_level ] ; sh:targetClass biolink:ChemicalToChemicalDerivationAssociation . biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; @@ -4906,25 +4906,56 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:description "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "the disease or phenotype that is affected by the chemical" ; sh:maxCount 1 ; @@ -4932,174 +4963,150 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 31 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ] ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An interaction between a chemical entity and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; @@ -5110,91 +5117,92 @@ biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:path rdf:object ] ; sh:targetClass biolink:ChemicalToEntityAssociationMixin . biolink:ChemicalToPathwayAssociation a sh:NodeShape ; sh:closed true ; sh:description "An interaction between a chemical entity and a biological process or pathway." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 35 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -5202,25 +5210,20 @@ biolink:ChemicalToPathwayAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -5230,21 +5233,34 @@ biolink:ChemicalToPathwayAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical entity that is affecting the pathway" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Pathway ; sh:description "the pathway that is affected by the chemical" ; sh:maxCount 1 ; @@ -5252,199 +5268,180 @@ biolink:ChemicalToPathwayAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical entity that is affecting the pathway" ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ] ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ] ; sh:targetClass biolink:ChemicalToPathwayAssociation . biolink:ChiSquaredAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a chi squared analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path biolink:license ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 10 ; sh:path biolink:category ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 2 ; + sh:path biolink:format ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:order 11 ; sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ] ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:ChiSquaredAnalysisResult . biolink:ClinicalCourse a sh:NodeShape ; sh:closed true ; sh:description "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 10 ; sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -5453,10 +5450,13 @@ biolink:ClinicalCourse a sh:NodeShape ; [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ] ; + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:ClinicalCourse . biolink:ClinicalEntity a sh:NodeShape ; @@ -5467,200 +5467,217 @@ biolink:ClinicalEntity a sh:NodeShape ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path dct:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ClinicalEntity . biolink:ClinicalFinding a sh:NodeShape ; sh:closed true ; sh:description "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:ClinicalAttribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:ClinicalFinding . - -biolink:ClinicalIntervention a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; sh:order 9 ; - sh:path dct:description ], + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ] ; + sh:targetClass biolink:ClinicalFinding . + +biolink:ClinicalIntervention a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:order 7 ; sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:iri ] ; sh:targetClass biolink:ClinicalIntervention . biolink:ClinicalMeasurement a sh:NodeShape ; sh:closed true ; sh:description "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -5668,51 +5685,38 @@ biolink:ClinicalMeasurement a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 10 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ] ; + sh:path biolink:category ] ; sh:targetClass biolink:ClinicalMeasurement . biolink:ClinicalModifier a sh:NodeShape ; sh:closed true ; sh:description "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -5720,20 +5724,39 @@ biolink:ClinicalModifier a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -5744,38 +5767,15 @@ biolink:ClinicalModifier a sh:NodeShape ; sh:maxCount 1 ; sh:order 12 ; sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ] ; + sh:order 13 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ClinicalModifier . biolink:ClinicalTrial a sh:NodeShape ; @@ -5785,17 +5785,6 @@ biolink:ClinicalTrial a sh:NodeShape ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 6 ; @@ -5804,95 +5793,106 @@ biolink:ClinicalTrial a sh:NodeShape ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 9 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ] ; + sh:path dct:description ] ; sh:targetClass biolink:ClinicalTrial . biolink:CodingSequence a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:xref ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:in_taxon_label ], - [ sh:description "connects a genomic feature to its sequence" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:order 8 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 6 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; sh:order 10 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 11 ; @@ -5903,64 +5903,64 @@ biolink:Cohort a sh:NodeShape ; sh:closed true ; sh:description "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; + sh:property [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:category ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ] ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ] ; sh:targetClass biolink:Cohort . biolink:CommonDataElement a sh:NodeShape ; @@ -5968,127 +5968,117 @@ biolink:CommonDataElement a sh:NodeShape ; sh:description "A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 10 ; sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 12 ; sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:format ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 1 ; - sh:path biolink:rights ] ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ] ; sh:targetClass biolink:CommonDataElement . biolink:ComplexChemicalExposure a sh:NodeShape ; sh:closed true ; sh:description "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 12 ; + sh:path dct:description ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "a long-form human readable name for a thing" ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -6096,196 +6086,168 @@ biolink:ComplexChemicalExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ] ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:ComplexChemicalExposure . biolink:ComplexMolecularMixture a sh:NodeShape ; sh:closed true ; sh:description "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path dct:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 10 ; sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:has_attribute ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_supplement ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:trade_name ], + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], + sh:description "" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:is_toxic ], + [ sh:datatype xsd:string ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:category ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 12 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:iri ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], + sh:description "" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:string ; sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 12 ; - sh:path biolink:synonym ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:datatype xsd:string ; - sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ] ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:ComplexMolecularMixture . biolink:ConceptCountAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a concept count analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 10 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 6 ; + sh:path biolink:full_name ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 3 ; - sh:path biolink:creation_date ] ; - sh:targetClass biolink:ConceptCountAnalysisResult . - -biolink:ConfidenceLevel a sh:NodeShape ; - sh:closed true ; - sh:description "Level of confidence in a statement" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 0 ; @@ -6293,6 +6255,17 @@ biolink:ConfidenceLevel a sh:NodeShape ; [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -6300,84 +6273,178 @@ biolink:ConfidenceLevel a sh:NodeShape ; sh:order 8 ; sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ] ; + sh:targetClass biolink:ConceptCountAnalysisResult . + +biolink:ConfidenceLevel a sh:NodeShape ; + sh:closed true ; + sh:description "Level of confidence in a statement" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 0 ; + sh:path biolink:license ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 7 ; sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:deprecated ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 12 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ] ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ] ; sh:targetClass biolink:ConfidenceLevel . biolink:ContributorAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -6385,111 +6452,66 @@ biolink:ContributorAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:InformationContentEntity ; + sh:description "information content entity which an agent has helped realise" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:class biolink:InformationContentEntity ; - sh:description "information content entity which an agent has helped realise" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "a point in time" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:Agent ; sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; sh:maxCount 1 ; @@ -6497,63 +6519,80 @@ biolink:ContributorAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ] ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ] ; sh:targetClass biolink:ContributorAssociation . biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:defaultValue "not_provided" ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 44 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 16 ; @@ -6563,37 +6602,38 @@ biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 42 ; sh:path biolink:has_total ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is shown to correlate with the disease." ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:double ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 35 ; sh:path biolink:category ], @@ -6602,268 +6642,228 @@ biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:minCount 1 ; + sh:order 33 ; + sh:path biolink:id ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 7 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_count ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 19 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 41 ; + sh:path biolink:has_count ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is shown to correlate with the disease." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 39 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 37 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], + sh:order 5 ; + sh:path biolink:sex_qualifier ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 18 ; sh:path biolink:original_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ] ; + sh:order 38 ; + sh:path dct:description ] ; sh:targetClass biolink:CorrelatedGeneToDiseaseAssociation . biolink:DatasetSummary a sh:NodeShape ; sh:closed true ; sh:description "an item that holds summary level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:format ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:creation_date ], + sh:order 15 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 10 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:license ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:license ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 14 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:rights ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:source_web_page ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:rights ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 1 ; sh:path schema1:logo ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:order 13 ; - sh:path rdf:type ], + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:format ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -6875,10 +6875,21 @@ biolink:DatasetVersion a sh:NodeShape ; sh:closed true ; sh:description "an item that holds version level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:ingest_date ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -6886,85 +6897,73 @@ biolink:DatasetVersion a sh:NodeShape ; sh:order 11 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 5 ; + sh:path biolink:format ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], + sh:order 16 ; + sh:path dct:description ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:creation_date ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ], [ sh:class biolink:DatasetDistribution ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path dct:distribution ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:license ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:format ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], + sh:order 18 ; + sh:path biolink:deprecated ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:rights ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:creation_date ], [ sh:class biolink:Dataset ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_dataset ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ] ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:DatasetVersion . biolink:DiagnosticAid a sh:NodeShape ; sh:closed true ; sh:description "A device or substance used to help diagnose disease or injury" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -6974,64 +6973,50 @@ biolink:DiagnosticAid a sh:NodeShape ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 9 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ] ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ] ; sh:targetClass biolink:DiagnosticAid . biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; sh:closed true ; sh:description "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:category ], @@ -7044,19 +7029,29 @@ biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -7064,29 +7059,34 @@ biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureExposure . biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; @@ -7098,18 +7098,18 @@ biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; @@ -7124,49 +7124,143 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape sh:description "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:GeneticInheritance ; + sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; @@ -7174,29 +7268,60 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . + +biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -7205,258 +7330,151 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape sh:order 12 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "a point in time" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:GeneticInheritance ; - sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . - -biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:class biolink:AnatomicalEntity ; sh:description "anatomical entity in which the disease or feature is found." ; sh:maxCount 1 ; @@ -7464,64 +7482,46 @@ biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ] ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:Disease ; sh:description "disease class" ; sh:maxCount 1 ; @@ -7536,17 +7536,34 @@ biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:description "An association between an exposure event and a disease." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -7554,116 +7571,76 @@ biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:Disease ; + sh:description "disease class" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:ExposureEvent ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 31 ; @@ -7673,56 +7650,79 @@ biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:ExposureEvent ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ] ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:DiseaseToExposureEventAssociation . biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; @@ -7730,84 +7730,41 @@ biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:description "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 36 ; - sh:path biolink:id ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_total ], + sh:order 10 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:negated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 38 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 16 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 22 ; + sh:path biolink:original_object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 37 ; + sh:path biolink:iri ], + [ sh:class biolink:Disease ; + sh:description "disease class" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 5 ; + sh:path rdf:subject ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category ], + sh:order 7 ; + sh:path rdf:object ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 38 ; + sh:path biolink:category ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; @@ -7817,166 +7774,209 @@ biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 19 ; sh:path biolink:timepoint ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 46 ; sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:deprecated ], + sh:order 2 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 16 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 39 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 18 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:has_attribute ], + sh:order 28 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:publications ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:onset_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 9 ; + sh:path biolink:negated ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path rdf:predicate ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:has_quotient ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:subject_namespace ], + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:subject_category_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 23 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 39 ; - sh:path rdf:type ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:onset_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path rdf:object ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:subject ], + sh:order 20 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 32 ; sh:path biolink:object_label_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 34 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:original_object ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 35 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 40 ; - sh:path rdfs:label ], + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 31 ; - sh:path biolink:subject_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:knowledge_level ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 30 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; + sh:order 21 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 36 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:deprecated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 31 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:p_value ] ; + sh:order 40 ; + sh:path rdfs:label ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:knowledge_level ] ; sh:targetClass biolink:DiseaseToPhenotypicFeatureAssociation . biolink:DrugExposure a sh:NodeShape ; @@ -7989,40 +7989,45 @@ biolink:DrugExposure a sh:NodeShape ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:category ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path biolink:has_quantitative_value ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 7 ; sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], + sh:order 2 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:order 12 ; sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -8030,86 +8035,44 @@ biolink:DrugExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_attribute_type ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 8 ; sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ] ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:DrugExposure . biolink:DrugLabel a sh:NodeShape ; sh:closed true ; sh:description "a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:order 6 ; sh:path dct:type ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:creation_date ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 17 ; + sh:path rdf:type ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 16 ; @@ -8125,33 +8088,70 @@ biolink:DrugLabel a sh:NodeShape ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:format ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:creation_date ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:iri ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; sh:order 3 ; sh:path biolink:keywords ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 11 ; sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:summary ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:id ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path rdfs:label ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 13 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:order 17 ; - sh:path rdf:type ] ; + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path dct:description ] ; sh:targetClass biolink:DrugLabel . biolink:DrugToEntityAssociationMixin a sh:NodeShape ; @@ -8183,38 +8183,72 @@ biolink:DrugToGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "An interaction between a drug and a gene or gene product." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:class biolink:Drug ; + sh:description "the drug that is an interactor" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the gene or gene product that is affected by the drug" ; sh:maxCount 1 ; @@ -8222,30 +8256,30 @@ biolink:DrugToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -8253,146 +8287,135 @@ biolink:DrugToGeneAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:class biolink:Drug ; - sh:description "the drug that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:path dct:description ] ; + sh:targetClass biolink:DrugToGeneAssociation . + +biolink:DrugToGeneInteractionExposure a sh:NodeShape ; + sh:closed true ; + sh:description "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], + [ sh:datatype xsd:string ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 5 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 9 ; + sh:path biolink:xref ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 11 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 36 ; + sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ] ; - sh:targetClass biolink:DrugToGeneAssociation . - -biolink:DrugToGeneInteractionExposure a sh:NodeShape ; - sh:closed true ; - sh:description "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 10 ; + sh:path biolink:full_name ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -8400,139 +8423,108 @@ biolink:DrugToGeneInteractionExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_attribute_type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 11 ; - sh:path biolink:synonym ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_qualitative_value ], + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 8 ; sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 9 ; - sh:path biolink:xref ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 3 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ] ; + sh:order 6 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:DrugToGeneInteractionExposure . biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 46 ; sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:double ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:description "a human-readable description of an entity" ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 47 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 41 ; + sh:path biolink:has_count ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], + sh:order 34 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:description "a point in time" ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:order 42 ; + sh:path biolink:has_total ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -8540,94 +8532,116 @@ biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:order 20 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_percentage ], + sh:order 33 ; + sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 35 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_count ], + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:p_value ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:description "connects an association to an instance of supporting evidence" ; sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; sh:order 10 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], + sh:order 38 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_closure ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 18 ; @@ -8637,100 +8651,71 @@ biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:subject_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 44 ; + sh:path biolink:has_percentage ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 15 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 35 ; - sh:path biolink:category ] ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:has_quotient ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:timepoint ] ; sh:targetClass biolink:DruggableGeneToDiseaseAssociation . biolink:Entity a sh:NodeShape ; sh:closed false ; sh:description "Root Biolink Model class for all things and informational relationships, real or imagined." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 2 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; sh:order 3 ; sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 2 ; + sh:path biolink:category ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 5 ; @@ -8738,7 +8723,22 @@ biolink:Entity a sh:NodeShape ; [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 4 ; - sh:path rdfs:label ] ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Entity . biolink:EntityToDiseaseAssociation a sh:NodeShape ; @@ -8748,220 +8748,225 @@ biolink:EntityToDiseaseAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 37 ; sh:path dct:description ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:object_closure ], + sh:order 26 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 30 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], + sh:order 31 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 39 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:description "a point in time" ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], + sh:order 5 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:object_category ], - [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:max_research_phase ], - [ sh:description "" ; - sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:clinical_approval_status ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 38 ; sh:path biolink:has_attribute ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:object_namespace ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:object_closure ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path rdf:predicate ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:order 8 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 12 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:max_research_phase ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:description "" ; + sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:clinical_approval_status ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 25 ; - sh:path biolink:subject_namespace ] ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ] ; sh:targetClass biolink:EntityToDiseaseAssociation . biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "mixin class for any association whose object (target node) is a disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 1 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], + sh:minCount 1 ; + sh:order 7 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 2 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -8973,11 +8978,6 @@ biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:frequency_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -8986,15 +8986,15 @@ biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; sh:order 8 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 4 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path rdf:predicate ] ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ] ; sh:targetClass biolink:EntityToDiseaseAssociationMixin . biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; @@ -9005,20 +9005,20 @@ biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ] ; + sh:path rdf:subject ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . biolink:EntityToExposureEventAssociationMixin a sh:NodeShape ; @@ -9050,25 +9050,37 @@ biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; sh:closed false ; sh:description "Qualifiers for entity to disease or phenotype associations." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualified_predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:frequency_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path rdf:subject ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:object_direction_qualifier ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -9076,42 +9088,23 @@ biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path rdf:predicate ], + sh:order 1 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 2 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:subject ] ; + sh:path biolink:object_aspect_qualifier ] ; sh:targetClass biolink:EntityToFeatureOrDiseaseQualifiersMixin . biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An association between some entity and an outcome" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Outcome ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -9122,87 +9115,98 @@ biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:predicate ], + [ sh:class biolink:Outcome ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:EntityToOutcomeAssociationMixin . biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 5 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:object_closure ], + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:timepoint ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:max_research_phase ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], + sh:order 2 ; + sh:path rdf:subject ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 34 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ], + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], + sh:order 20 ; + sh:path biolink:object_category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -9210,206 +9214,227 @@ biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path rdf:object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:max_research_phase ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 25 ; sh:path biolink:subject_namespace ], - [ sh:description "" ; - sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:clinical_approval_status ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], + sh:order 24 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 31 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:p_value ], + sh:order 37 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 39 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category_closure ], + [ sh:description "" ; + sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 0 ; + sh:path biolink:clinical_approval_status ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:subject_closure ], + sh:order 30 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ] ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:EntityToPhenotypicFeatureAssociation . biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:has_total ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 12 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:object_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:has_percentage ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 13 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:qualified_predicate ] ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:has_count ] ; sh:targetClass biolink:EntityToPhenotypicFeatureAssociationMixin . biolink:EnvironmentalExposure a sh:NodeShape ; sh:closed true ; sh:description "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:category ], @@ -9417,138 +9442,111 @@ biolink:EnvironmentalExposure a sh:NodeShape ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 7 ; sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:order 12 ; sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; - sh:path biolink:has_quantitative_value ] ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ] ; sh:targetClass biolink:EnvironmentalExposure . biolink:EnvironmentalFeature a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ] ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ] ; sh:targetClass biolink:EnvironmentalFeature . biolink:EnvironmentalFoodContaminant a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 3 ; + sh:path biolink:is_toxic ], + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -9559,113 +9557,115 @@ biolink:EnvironmentalFoodContaminant a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:trade_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:max_tolerated_dose ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 5 ; sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path dct:description ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_toxic ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ] ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:trade_name ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:EnvironmentalFoodContaminant . biolink:EnvironmentalProcess a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 9 ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 7 ; + sh:path rdf:type ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 3 ; sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ] ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ] ; sh:targetClass biolink:EnvironmentalProcess . biolink:EpidemiologicalOutcome a sh:NodeShape ; @@ -9687,131 +9687,109 @@ biolink:Event a sh:NodeShape ; sh:closed true ; sh:description "Something that happens at a given place and time." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:category ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 3 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 9 ; sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ] ; + sh:order 11 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:Event . biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:closed true ; sh:description "A transcript is formed from multiple exons" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Exon ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Transcript ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -9819,509 +9797,389 @@ biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Exon ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 30 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:class biolink:Transcript ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; - sh:path biolink:retrieval_source_ids ] ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ] ; sh:targetClass biolink:ExonToTranscriptRelationship . biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between an exposure event and an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:p_value ], - [ sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:temporal_context_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], + sh:order 2 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 25 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 35 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; - sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:population_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 36 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:description "a point in time" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:population_context_qualifier ], + [ sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 1 ; + sh:path biolink:temporal_context_qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 38 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 29 ; sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Outcome ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ] ; - sh:targetClass biolink:ExposureEventToOutcomeAssociation . - -biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; + sh:order 32 ; sh:path biolink:id ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_quotient ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:path biolink:subject_category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 37 ; + sh:path dct:description ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:class biolink:Outcome ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 4 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; + sh:order 28 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:ExposureEvent ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:has_total ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; + sh:order 22 ; sh:path biolink:object_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 29 ; + sh:order 30 ; sh:path biolink:p_value ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; + sh:order 27 ; sh:path biolink:subject_label_closure ], - [ sh:description "a point in time" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_percentage ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 6 ; + sh:path biolink:qualifier ] ; + sh:targetClass biolink:ExposureEventToOutcomeAssociation . + +biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:order 48 ; + sh:path biolink:frequency_qualifier ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 39 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 34 ; sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 46 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:category ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -10329,90 +10187,208 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:agent_type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 44 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:has_total ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 36 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:negated ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 45 ; sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:has_count ] ; - sh:targetClass biolink:ExposureEventToPhenotypicFeatureAssociation . - -biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; - sh:closed false ; - sh:description "Qualifiers for disease or phenotype to entity associations." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 41 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 0 ; + sh:order 43 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:ExposureEvent ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:qualified_predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path rdf:predicate ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:NamedThing ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; + sh:targetClass biolink:ExposureEventToPhenotypicFeatureAssociation . + +biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; + sh:closed false ; + sh:description "Qualifiers for disease or phenotype to entity associations." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -10424,160 +10400,180 @@ biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:subject_direction_qualifier ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path rdf:object ] ; + sh:path rdf:object ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path rdf:predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:object_aspect_qualifier ] ; sh:targetClass biolink:FeatureOrDiseaseQualifiersToEntityMixin . biolink:Food a sh:NodeShape ; sh:closed true ; sh:description "A substance consumed by a living organism as a source of nutrition" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:class biolink:ChemicalRole ; + sh:property [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_chemical_role ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 12 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ], + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:is_supplement ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:order 16 ; sh:path rdf:type ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:string ; - sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 12 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:is_toxic ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:trade_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:full_name ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ] ; + sh:order 18 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:Food . biolink:FoodAdditive a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_chemical_role ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path biolink:trade_name ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:full_name ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:id ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 14 ; @@ -10587,26 +10583,30 @@ biolink:FoodAdditive a sh:NodeShape ; sh:order 10 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], + sh:order 12 ; + sh:path rdf:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:trade_name ], + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; @@ -10618,11 +10618,10 @@ biolink:FrequencyQualifierMixin a sh:NodeShape ; sh:closed false ; sh:description "Qualifier for frequency type associations" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:order 0 ; + sh:path biolink:frequency_qualifier ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -10630,10 +10629,11 @@ biolink:FrequencyQualifierMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:frequency_qualifier ], + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -10646,7 +10646,11 @@ biolink:FrequencyQualifierMixin a sh:NodeShape ; biolink:FrequencyQuantifier a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:integer ; + sh:property [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:order 1 ; @@ -10656,10 +10660,6 @@ biolink:FrequencyQuantifier a sh:NodeShape ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_count ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_quotient ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; @@ -10671,150 +10671,76 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 32 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -10822,171 +10748,223 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "a point in time" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; - sh:path biolink:object_label_closure ] ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ] ; sh:targetClass biolink:FunctionalAssociation . biolink:Fungus a sh:NodeShape ; sh:closed true ; sh:description "A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:Fungus . biolink:GeneAffectsChemicalAssociation a sh:NodeShape ; sh:closed true ; sh:description "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:subject_context_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 27 ; - sh:path biolink:knowledge_level ], + sh:order 45 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 35 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 41 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 49 ; - sh:path rdf:type ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 36 ; + sh:path biolink:object_closure ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:causal_mechanism_qualifier ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 52 ; - sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 37 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; + sh:in ( "metabolite" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 28 ; - sh:path biolink:agent_type ], + sh:order 11 ; + sh:path biolink:object_derivative_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:original_object ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 42 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:original_subject ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path rdf:object ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 35 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -10994,73 +10972,60 @@ biolink:GeneAffectsChemicalAssociation a sh:NodeShape ; sh:order 34 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 42 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:knowledge_source ], + sh:order 32 ; + sh:path biolink:original_object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 36 ; - sh:path biolink:object_closure ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:qualified_predicate ], + sh:minCount 1 ; + sh:order 46 ; + sh:path biolink:id ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 44 ; sh:path biolink:p_value ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:object_part_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 29 ; + sh:path biolink:timepoint ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 46 ; - sh:path biolink:id ], - [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; - sh:in ( "metabolite" ) ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:object_derivative_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 28 ; + sh:path biolink:agent_type ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 17 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:negated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path rdf:object ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 48 ; + sh:path biolink:category ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:AnatomicalEntity ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:object_context_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:qualifiers ], + sh:order 51 ; + sh:path dct:description ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -11068,310 +11033,237 @@ biolink:GeneAffectsChemicalAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 16 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:object_namespace ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 26 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 43 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 51 ; - sh:path dct:description ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 52 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:qualifier ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 48 ; - sh:path biolink:category ], + sh:minCount 1 ; + sh:order 27 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 53 ; sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 50 ; - sh:path rdfs:label ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:species_context_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:publications ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:subject_category ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:order 4 ; + sh:path biolink:subject_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:order 25 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:causal_mechanism_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 19 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:iri ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:order 40 ; + sh:path biolink:object_namespace ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 7 ; + sh:path biolink:object_part_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:qualified_predicate ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 23 ; + sh:path biolink:has_evidence ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], + sh:order 50 ; + sh:path rdfs:label ], [ sh:class biolink:AnatomicalEntity ; sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:anatomical_context_qualifier ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:species_context_qualifier ] ; - sh:targetClass biolink:GeneAffectsChemicalAssociation . - -biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], + sh:order 38 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 41 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "a point in time" ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 26 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 11 ; + sh:order 24 ; sh:path biolink:knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 43 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 33 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:description "The relationship to the disease" ; + sh:order 5 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 8 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], + sh:order 6 ; + sh:path biolink:object_form_or_variant_qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], + sh:order 30 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 21 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 9 ; - sh:path biolink:publications ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], + sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 49 ; + sh:path rdf:type ] ; + sh:targetClass biolink:GeneAffectsChemicalAssociation . + +biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 34 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 26 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 44 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "The relationship to the disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -11379,43 +11271,93 @@ biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:agent_type ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_total ], + sh:order 38 ; + sh:path dct:description ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 37 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 35 ; sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; sh:maxCount 1 ; @@ -11423,23 +11365,81 @@ biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:has_count ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 28 ; sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_total ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "a human-readable description of an entity" ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -11452,30 +11452,30 @@ biolink:GeneExpressionMixin a sh:NodeShape ; sh:closed false ; sh:description "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Optional quantitative value indicating degree of expression." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:phenotypic_state ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], [ sh:class biolink:LifeStage ; sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:stage_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ] ; + sh:order 1 ; + sh:path biolink:expression_site ] ; sh:targetClass biolink:GeneExpressionMixin . biolink:GeneGroupingMixin a sh:NodeShape ; @@ -11492,109 +11492,178 @@ biolink:GeneGroupingMixin a sh:NodeShape ; biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:order 48 ; sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 34 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 27 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 7 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 6 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:qualifier ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 36 ; + sh:path biolink:category ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 34 ; - sh:path biolink:id ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 20 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 44 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 14 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], + sh:order 45 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 37 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:object_category_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:has_total ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:deprecated ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -11602,65 +11671,60 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:has_percentage ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 46 ; sh:path biolink:subject_direction_qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:label ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], + sh:order 22 ; + sh:path biolink:object_category ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 39 ; sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; @@ -11670,165 +11734,235 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 35 ; sh:path biolink:iri ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_predicate ], + sh:order 32 ; + sh:path biolink:p_value ] ; + sh:targetClass biolink:GeneHasVariantThatContributesToDiseaseAssociation . + +biolink:GeneProductIsoformMixin a sh:NodeShape ; + sh:closed false ; + sh:description "This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:GeneProductIsoformMixin . + +biolink:GeneToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:p_value ], [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 17 ; + sh:order 16 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:double ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_quotient ], + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 20 ; + sh:order 19 ; sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 5 ; sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 44 ; + sh:path biolink:has_percentage ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 9 ; + sh:order 8 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:subject_label_closure ] ; - sh:targetClass biolink:GeneHasVariantThatContributesToDiseaseAssociation . - -biolink:GeneProductIsoformMixin a sh:NodeShape ; - sh:closed false ; - sh:description "This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:GeneProductIsoformMixin . - -biolink:GeneToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 42 ; + sh:path biolink:has_total ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:order 41 ; sh:path biolink:has_count ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 33 ; + sh:path biolink:id ], [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:order 43 ; sh:path biolink:has_quotient ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 27 ; sh:path biolink:object_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 35 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -11839,429 +11973,288 @@ biolink:GeneToDiseaseAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_total ], + sh:order 15 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:subject_category ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], + sh:order 26 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:path biolink:original_subject ] ; + sh:targetClass biolink:GeneToDiseaseAssociation . + +biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], + sh:order 37 ; + sh:path rdfs:label ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_percentage ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:order 33 ; + sh:path biolink:id ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the phenotypic feature" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 35 ; - sh:path biolink:category ], + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 40 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:order 6 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ] ; - sh:targetClass biolink:GeneToDiseaseAssociation . - -biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_total ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 19 ; sh:path biolink:original_object ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:order 47 ; sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 29 ; sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], + sh:order 10 ; + sh:path biolink:has_evidence ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 39 ; sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the phenotypic feature" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_percentage ], + sh:order 1 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:object_namespace ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_count ], + sh:order 17 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], + sh:order 48 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 26 ; sh:path biolink:subject_namespace ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 35 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 44 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:deprecated ] ; + sh:order 41 ; + sh:path biolink:has_count ] ; sh:targetClass biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . biolink:GeneToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:GeneOrGeneProduct ; + sh:property [ sh:class biolink:GeneOrGeneProduct ; sh:description "gene that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -12272,107 +12265,133 @@ biolink:GeneToEntityAssociationMixin a sh:NodeShape ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:GeneToEntityAssociationMixin . biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:LifeStage ; - sh:description "stage at which the gene is expressed in the site" ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:stage_qualifier ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "can be used to indicate magnitude, or also ranking" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:quantifier_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 19 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], + sh:order 25 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 38 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 5 ; + sh:path biolink:negated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ], + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 30 ; sh:path biolink:p_value ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path dct:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which the gene is expressed" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; @@ -12383,64 +12402,43 @@ biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_label_closure ], + sh:order 31 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:subject_closure ], + sh:order 39 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:description "expression relationship" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:minCount 1 ; + sh:order 3 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which the gene is expressed" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_predicate ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." ; sh:maxCount 1 ; @@ -12448,51 +12446,46 @@ biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 34 ; + sh:path biolink:category ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 33 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:LifeStage ; + sh:description "stage at which the gene is expressed in the site" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "expression relationship" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:stage_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "can be used to indicate magnitude, or also ranking" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 1 ; + sh:path biolink:quantifier_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ] ; + sh:order 20 ; + sh:path biolink:object_category ] ; sh:targetClass biolink:GeneToExpressionSiteAssociation . biolink:GeneToGeneAssociation a sh:NodeShape ; sh:closed false ; sh:description "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; + sh:property [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; @@ -12502,15 +12495,24 @@ biolink:GeneToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -12519,32 +12521,75 @@ biolink:GeneToGeneAssociation a sh:NodeShape ; sh:order 11 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -12552,96 +12597,71 @@ biolink:GeneToGeneAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -12649,75 +12669,41 @@ biolink:GeneToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ] ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:GeneToGeneAssociation . biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; sh:closed true ; sh:description "Indicates that two genes are co-expressed, generally under the same conditions." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 32 ; sh:path biolink:p_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path dct:description ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -12728,208 +12714,254 @@ biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:label ], + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 4 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 40 ; sh:path biolink:has_attribute ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:negated ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], + sh:order 15 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:stage_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 37 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path rdf:predicate ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 34 ; - sh:path biolink:id ], + sh:order 17 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:expression_site ], [ sh:class biolink:OntologyClass ; sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:quantifier_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:description "a point in time" ; + sh:order 20 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 36 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], + sh:order 19 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_object ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:negated ], + sh:order 38 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 6 ; + sh:path rdf:object ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:phenotypic_state ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:phenotypic_state ] ; + sh:targetClass biolink:GeneToGeneCoexpressionAssociation . + +biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "membership of the gene in the given gene family." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 6 ; - sh:path rdf:object ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:object_label_closure ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:GeneFamily ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 8 ; + sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:Gene ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ] ; - sh:targetClass biolink:GeneToGeneCoexpressionAssociation . - -biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -12937,227 +12969,206 @@ biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 30 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 32 ; sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:iri ], - [ sh:description "membership of the gene in the given gene family." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 35 ; sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:GeneFamily ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ] ; + sh:order 3 ; + sh:path biolink:negated ] ; sh:targetClass biolink:GeneToGeneFamilyAssociation . biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; sh:closed true ; sh:description "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:description "homology relationship type" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "homology relationship type" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -13169,390 +13180,332 @@ biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:iri ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 35 ; + sh:path dct:description ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ] ; + sh:order 23 ; + sh:path biolink:subject_namespace ] ; sh:targetClass biolink:GeneToGeneHomologyAssociation . biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:closed true ; sh:description "A gene is transcribed and potentially translated to a gene product" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:GeneProductMixin ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "a point in time" ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:GeneProductMixin ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 30 ; + sh:path biolink:id ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; - sh:path biolink:retrieval_source_ids ] ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ] ; sh:targetClass biolink:GeneToGeneProductRelationship . biolink:GeneToGoTermAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 35 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:Gene ; sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; @@ -13560,101 +13513,138 @@ biolink:GeneToGoTermAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -13662,99 +13652,88 @@ biolink:GeneToGoTermAssociation a sh:NodeShape ; sh:order 18 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ] ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ] ; sh:targetClass biolink:GeneToGoTermAssociation . biolink:GeneToPathwayAssociation a sh:NodeShape ; sh:closed true ; sh:description "An interaction between a gene or gene product and a biological process or pathway." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:property [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:class biolink:Pathway ; + sh:description "the pathway that includes or is affected by the gene or gene product" ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -13762,13 +13741,16 @@ biolink:GeneToPathwayAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 35 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the gene or gene product entity that participates or influences the pathway" ; sh:maxCount 1 ; @@ -13776,352 +13758,367 @@ biolink:GeneToPathwayAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:class biolink:Pathway ; - sh:description "the pathway that includes or is affected by the gene or gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ] ; + sh:order 4 ; + sh:path biolink:qualifier ] ; sh:targetClass biolink:GeneToPathwayAssociation . biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], + sh:order 4 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], + sh:order 25 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 38 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:double ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 5 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:order 41 ; sh:path biolink:has_count ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_total ], + sh:order 11 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:object_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 42 ; + sh:path biolink:has_total ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 45 ; sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], + sh:order 39 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], + sh:order 7 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], + sh:order 27 ; + sh:path biolink:object_namespace ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:timepoint ], [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 35 ; - sh:path biolink:category ], + sh:order 43 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:order 47 ; sh:path biolink:qualified_predicate ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:deprecated ], + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], + sh:minCount 1 ; + sh:order 33 ; + sh:path biolink:id ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 35 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_closure ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 37 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], + sh:order 18 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 13 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 44 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "gene in which variation is correlated with the phenotypic feature" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ] ; + sh:path rdf:subject ] ; sh:targetClass biolink:GeneToPhenotypicFeatureAssociation . biolink:Genome a sh:NodeShape ; sh:closed true ; sh:description "A genome is the sum of genetic material within a cell or virion." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -14130,93 +14127,65 @@ biolink:Genome a sh:NodeShape ; [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 12 ; + sh:path dct:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:description "connects a genomic feature to its sequence" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:Genome . - -biolink:GenomicBackgroundExposure a sh:NodeShape ; - sh:closed true ; - sh:description "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 8 ; - sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:order 16 ; + sh:order 10 ; sh:path rdf:type ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:description "Alternate human-readable names for a thing" ; sh:order 7 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], + sh:path biolink:synonym ] ; + sh:targetClass biolink:Genome . + +biolink:GenomicBackgroundExposure a sh:NodeShape ; + sh:closed true ; + sh:description "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:has_attribute ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 13 ; @@ -14226,10 +14195,26 @@ biolink:GenomicBackgroundExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_gene_or_gene_product ], - [ sh:description "connects a genomic feature to its sequence" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 8 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -14240,36 +14225,51 @@ biolink:GenomicBackgroundExposure a sh:NodeShape ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 12 ; - sh:path biolink:xref ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:in_taxon_label ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_qualitative_value ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 14 ; + sh:path biolink:synonym ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 12 ; + sh:path biolink:xref ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:has_attribute ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 7 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 14 ; - sh:path biolink:synonym ] ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 11 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:GenomicBackgroundExposure . biolink:GenomicEntity a sh:NodeShape ; @@ -14285,112 +14285,108 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:closed true ; sh:description "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], - [ sh:description "a point in time" ; + sh:property [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:timepoint ], + sh:order 34 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a human-readable description of an entity" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 37 ; - sh:path biolink:category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], + sh:order 0 ; + sh:path biolink:start_interbase_coordinate ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 31 ; sh:path biolink:object_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:description "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; - sh:in ( "+" "-" "." "?" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:genome_build ], + sh:order 12 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_subject ], + sh:order 21 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], + sh:order 23 ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 35 ; sh:path biolink:id ], - [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; - sh:in ( "0" "1" "2" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:phase ], + sh:order 33 ; + sh:path biolink:p_value ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path dct:description ], + [ sh:datatype xsd:integer ; + sh:description "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:end_interbase_coordinate ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 15 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; - sh:in ( "+" "-" "." "?" ) ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:strand ], - [ sh:datatype xsd:integer ; - sh:description "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; + sh:order 13 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:start_interbase_coordinate ], + sh:order 29 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:negated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 24 ; @@ -14400,37 +14396,66 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:iri ], + sh:order 19 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 38 ; + sh:path rdf:type ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path rdf:predicate ], [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 7 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 9 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; + sh:in ( "0" "1" "2" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:phase ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path rdf:predicate ], + sh:order 17 ; + sh:path biolink:agent_type ], + [ sh:description "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; + sh:in ( "+" "-" "." "?" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:genome_build ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:timepoint ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -14438,284 +14463,259 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:minCount 1 ; sh:order 16 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:integer ; - sh:description "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:end_interbase_coordinate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 41 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 22 ; + sh:path biolink:subject_category ], + [ sh:description "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; + sh:in ( "+" "-" "." "?" ) ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:original_object ], + sh:order 3 ; + sh:path biolink:strand ], [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 5 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 42 ; + sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 37 ; + sh:path biolink:category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_source ] ; + sh:order 36 ; + sh:path biolink:iri ] ; sh:targetClass biolink:GenomicSequenceLocalization . biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "The relationship to the disease" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Genotype ; - sh:description "A genotype that has a role in modeling the disease." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "The relationship to the disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_direction_qualifier ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 43 ; sh:path biolink:frequency_qualifier ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 38 ; sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 40 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 39 ; sh:path biolink:subject_direction_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Genotype ; + sh:description "A genotype that has a role in modeling the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; @@ -14726,83 +14726,119 @@ biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:Genotype ; - sh:description "a genotype that is associated in some way with a disease state" ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:order 39 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 43 ; sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 41 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "E.g. is pathogenic for" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], [ sh:class biolink:Disease ; sh:description "a disease that is associated with that genotype" ; sh:maxCount 1 ; @@ -14810,502 +14846,409 @@ biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "E.g. is pathogenic for" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:Genotype ; + sh:description "a genotype that is associated in some way with a disease state" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 35 ; sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 38 ; sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 42 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ] ; + sh:order 28 ; + sh:path biolink:p_value ] ; sh:targetClass biolink:GenotypeToDiseaseAssociation . biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Genotype ; + sh:property [ sh:class biolink:Genotype ; sh:description "genotype that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:GenotypeToEntityAssociationMixin . - -biolink:GenotypeToGeneAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path rdf:subject ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; + sh:targetClass biolink:GenotypeToEntityAssociationMixin . + +biolink:GenotypeToGeneAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 32 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "the relationship type used to connect genotype to gene" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:description "the relationship type used to connect genotype to gene" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Gene ; - sh:description "gene implicated in genotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:GenotypeToGeneAssociation . - -biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Any association between one genotype and a genotypic entity that is a sub-component of it" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:Genotype ; - sh:description "child genotype" ; + sh:description "parent genotype" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Gene ; + sh:description "gene implicated in genotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; + sh:targetClass biolink:GenotypeToGeneAssociation . + +biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Any association between one genotype and a genotypic entity that is a sub-component of it" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:Genotype ; + sh:description "child genotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 30 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 32 ; sh:path biolink:category ], @@ -15314,430 +15257,505 @@ biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 35 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ] ; - sh:targetClass biolink:GenotypeToGenotypePartAssociation . - -biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 4 ; + sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:double ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_quotient ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 30 ; + sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; - sh:path biolink:primary_knowledge_source ], + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:description "a point in time" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:path biolink:original_subject ] ; + sh:targetClass biolink:GenotypeToGenotypePartAssociation . + +biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path dct:description ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:Genotype ; + sh:description "genotype that is associated with the phenotypic feature" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 46 ; sh:path biolink:object_direction_qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:has_count ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 44 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Genotype ; - sh:description "genotype that is associated with the phenotypic feature" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 48 ; sh:path biolink:frequency_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:has_total ], + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 25 ; sh:path biolink:object_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:has_total ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:has_count ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:sex_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_percentage ], - [ sh:description "a human-readable description of an entity" ; + sh:order 41 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ] ; + sh:order 37 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:GenotypeToPhenotypicFeatureAssociation . biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between a genotype and a sequence variant." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:SequenceVariant ; - sh:description "gene implicated in genotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "a human-readable description of an entity" ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + [ sh:description "the relationship type used to connect genotype to gene" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "the relationship type used to connect genotype to gene" ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:SequenceVariant ; + sh:description "gene implicated in genotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -15745,57 +15763,39 @@ biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 35 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ] ; + sh:order 15 ; + sh:path biolink:original_predicate ] ; sh:targetClass biolink:GenotypeToVariantAssociation . biolink:GenotypicSex a sh:NodeShape ; @@ -15805,20 +15805,30 @@ biolink:GenotypicSex a sh:NodeShape ; sh:property [ sh:datatype xsd:string ; sh:order 11 ; sh:path rdf:type ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 0 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -15830,92 +15840,81 @@ biolink:GenotypicSex a sh:NodeShape ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:QuantityValue ; + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ] ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:GenotypicSex . biolink:GeographicExposure a sh:NodeShape ; sh:closed true ; sh:description "A geographic exposure is a factor relating to geographic proximity to some impactful entity." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], + sh:order 2 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:order 12 ; sh:path rdf:type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 8 ; sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -15924,206 +15923,172 @@ biolink:GeographicExposure a sh:NodeShape ; [ sh:description "Alternate human-readable names for a thing" ; sh:order 10 ; sh:path biolink:synonym ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; - sh:path biolink:id ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:id ] ; sh:targetClass biolink:GeographicExposure . biolink:GeographicLocation a sh:NodeShape ; sh:closed true ; sh:description "a location that can be described in lat/long coordinates" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:float ; - sh:description "latitude" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:latitude ], - [ sh:datatype xsd:float ; - sh:description "longitude" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:longitude ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:float ; + sh:description "longitude" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:longitude ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:float ; + sh:description "latitude" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 0 ; + sh:path biolink:latitude ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path dct:description ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; - sh:path biolink:full_name ] ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:GeographicLocation . biolink:GeographicLocationAtTime a sh:NodeShape ; sh:closed true ; sh:description "a location that can be described in lat/long coordinates, for a particular time" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:id ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:float ; + sh:description "latitude" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:latitude ], [ sh:datatype xsd:float ; sh:description "longitude" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:longitude ], - [ sh:datatype xsd:float ; - sh:description "latitude" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:latitude ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 6 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:full_name ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 9 ; - sh:path biolink:category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ] ; + sh:path biolink:category ] ; sh:targetClass biolink:GeographicLocationAtTime . biolink:GrossAnatomicalStructure a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; @@ -16135,34 +16100,77 @@ biolink:GrossAnatomicalStructure a sh:NodeShape ; [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ] ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ] ; sh:targetClass biolink:GrossAnatomicalStructure . biolink:Haplotype a sh:NodeShape ; sh:closed true ; sh:description "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 11 ; @@ -16170,101 +16178,93 @@ biolink:Haplotype a sh:NodeShape ; [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; sh:path dct:description ], [ sh:datatype xsd:string ; sh:order 10 ; - sh:path rdf:type ] ; - sh:targetClass biolink:Haplotype . - -biolink:Hospitalization a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; + sh:order 4 ; sh:path biolink:provided_by ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 5 ; + sh:order 8 ; sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + sh:order 9 ; + sh:path biolink:category ] ; + sh:targetClass biolink:Haplotype . + +biolink:Hospitalization a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; - sh:path biolink:xref ] ; + sh:path biolink:xref ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ] ; sh:targetClass biolink:Hospitalization . biolink:HospitalizationOutcome a sh:NodeShape ; @@ -16277,89 +16277,113 @@ biolink:Human a sh:NodeShape ; sh:closed true ; sh:description "A member of the the species Homo sapiens." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ] ; + sh:path rdfs:label ] ; sh:targetClass biolink:Human . biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:closed true ; sh:description "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -16367,11 +16391,25 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:order 18 ; sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -16379,125 +16417,92 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -16505,51 +16510,72 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ] ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:InformationContentEntityToNamedThingAssociation . biolink:Invertebrate a sh:NodeShape ; sh:closed true ; sh:description "An animal lacking a vertebral column. This group consists of 98% of all animal species." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], @@ -16558,104 +16584,92 @@ biolink:Invertebrate a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ] ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:Invertebrate . biolink:JournalArticle a sh:NodeShape ; sh:closed true ; sh:description "an article, typically presenting results of research, that is published in an issue of a scientific journal." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 9 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:full_name ], + sh:order 25 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:volume ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 20 ; + sh:path biolink:category ], [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; sh:path biolink:published_in ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:deprecated ], + sh:order 16 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:order 10 ; + sh:path dct:type ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:iso_abbreviation ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 9 ; - sh:path biolink:xref ], + sh:order 23 ; + sh:path dct:description ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 17 ; + sh:path biolink:synonym ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:authors ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 20 ; - sh:path biolink:category ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:has_attribute ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 8 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 5 ; + sh:path biolink:pages ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:issue ], + sh:order 14 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:order 21 ; + sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 19 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:summary ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 5 ; - sh:path biolink:pages ], [ sh:datatype xsd:string ; sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; @@ -16663,97 +16677,51 @@ biolink:JournalArticle a sh:NodeShape ; sh:order 18 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 10 ; - sh:path dct:type ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:creation_date ], + sh:order 1 ; + sh:path biolink:iso_abbreviation ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; sh:order 7 ; sh:path biolink:keywords ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:rights ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 17 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:order 21 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:has_attribute ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 8 ; - sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 15 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:format ], + sh:order 12 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:volume ] ; + sh:order 3 ; + sh:path biolink:issue ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:format ] ; sh:targetClass biolink:JournalArticle . biolink:LogOddsAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a log odds ratio analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -16767,161 +16735,218 @@ biolink:LogOddsAnalysisResult a sh:NodeShape ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:license ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 10 ; sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ] ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ] ; sh:targetClass biolink:LogOddsAnalysisResult . biolink:MacromolecularComplex a sh:NodeShape ; sh:closed true ; sh:description "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], + sh:order 9 ; + sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 6 ; + sh:path biolink:synonym ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:full_name ] ; + sh:targetClass biolink:MacromolecularComplex . + +biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:MacromolecularComplex . - -biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:class biolink:BiologicalProcess ; sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; @@ -16930,181 +16955,108 @@ biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; sh:order 2 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:iri ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ] ; + sh:path dct:description ] ; sh:targetClass biolink:MacromolecularMachineToBiologicalProcessAssociation . biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:closed true ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:CellularComponent ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -17115,28 +17067,9 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:order 34 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; @@ -17146,24 +17079,15 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -17175,41 +17099,63 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:description "a point in time" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -17217,11 +17163,44 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -17229,12 +17208,33 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:CellularComponent ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ] ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:MacromolecularMachineToCellularComponentAssociation . biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; @@ -17246,278 +17246,278 @@ biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 0 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:MacromolecularMachineToEntityAssociationMixin . + +biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:MolecularActivity ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; - sh:targetClass biolink:MacromolecularMachineToEntityAssociationMixin . - -biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "a point in time" ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "a human-readable description of an entity" ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 35 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 23 ; + sh:path biolink:subject_namespace ] ; + sh:targetClass biolink:MacromolecularMachineToMolecularActivityAssociation . + +biolink:Mammal a sh:NodeShape ; + sh:closed true ; + sh:description "A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:MolecularActivity ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ] ; - sh:targetClass biolink:MacromolecularMachineToMolecularActivityAssociation . - -biolink:Mammal a sh:NodeShape ; - sh:closed true ; - sh:description "A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ] ; + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Mammal . biolink:MappingCollection a sh:NodeShape ; @@ -17536,110 +17536,147 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:description "An association between a material sample and the material entity from which it is derived." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "derivation relationship" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:MaterialSample ; - sh:description "the material sample being described" ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:description "derivation relationship" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 35 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:MaterialSample ; + sh:description "the material sample being described" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -17647,18 +17684,10 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:order 30 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:NamedThing ; sh:description "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material." ; sh:maxCount 1 ; @@ -17666,84 +17695,101 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ] ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ] ; sh:targetClass biolink:MaterialSampleDerivationAssociation . biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a material sample and a disease or phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:property [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -17752,145 +17798,105 @@ biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 12 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 35 ; sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 31 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:MaterialSample ; sh:description "the material sample being described" ; sh:maxCount 1 ; @@ -17898,25 +17904,19 @@ biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ] ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ] ; sh:targetClass biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; @@ -17947,33 +17947,19 @@ biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; biolink:MicroRNA a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; + sh:property [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:full_name ], [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 10 ; @@ -17983,35 +17969,54 @@ biolink:MicroRNA a sh:NodeShape ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ] ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:MicroRNA . biolink:ModelToDiseaseAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:description "The relationship to the disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; sh:description "The entity that serves as the model of the disease. This may be an organism, a strain of organism, a genotype or variant that exhibits similar features, or a gene that when mutated exhibits features of the disease" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -18024,193 +18029,128 @@ biolink:ModelToDiseaseAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ], - [ sh:description "The relationship to the disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:object ] ; sh:targetClass biolink:ModelToDiseaseAssociationMixin . biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:closed true ; sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 35 ; sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 30 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -18218,43 +18158,28 @@ biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ] ; - sh:targetClass biolink:MolecularActivityToChemicalEntityAssociation . - -biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -18262,271 +18187,268 @@ biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ] ; + sh:targetClass biolink:MolecularActivityToChemicalEntityAssociation . + +biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ] ; - sh:targetClass biolink:MolecularActivityToMolecularActivityAssociation . - -biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Association that holds the relationship between a reaction and the pathway it participates in." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 30 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Pathway ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:MolecularActivity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "a point in time" ; + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 13 ; + sh:path biolink:timepoint ] ; + sh:targetClass biolink:MolecularActivityToMolecularActivityAssociation . + +biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Association that holds the relationship between a reaction and the pathway it participates in." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Pathway ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:MolecularActivity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -18534,182 +18456,260 @@ biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ] ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ] ; sh:targetClass biolink:MolecularActivityToPathwayAssociation . biolink:MolecularMixture a sh:NodeShape ; sh:closed true ; sh:description "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ], + sh:order 14 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], + sh:order 17 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 12 ; + sh:path biolink:synonym ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:has_attribute ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:full_name ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:category ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:order 0 ; + sh:path biolink:is_supplement ], [ sh:datatype xsd:string ; - sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:trade_name ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 12 ; - sh:path biolink:synonym ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 18 ; sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:string ; - sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ] ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ] ; sh:targetClass biolink:MolecularMixture . biolink:MortalityOutcome a sh:NodeShape ; @@ -18722,119 +18722,59 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:order 7 ; + sh:path biolink:population_context_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:original_object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], + sh:order 23 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:subject_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 33 ; sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:subject_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 37 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], + sh:order 27 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 31 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:qualifier ], + sh:order 13 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -18843,54 +18783,98 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_subject ], + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:population_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 4 ; + sh:path rdf:object ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_evidence ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 19 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:negated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], + sh:order 2 ; + sh:path biolink:subject_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 38 ; + sh:path rdf:type ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], + sh:order 22 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:subject_namespace ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -18898,246 +18882,284 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:minCount 1 ; sh:order 17 ; sh:path biolink:agent_type ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:object_context_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 35 ; sh:path biolink:id ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ] ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 37 ; + sh:path biolink:category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:original_predicate ] ; sh:targetClass biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . biolink:NoncodingRNAProduct a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path dct:description ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ] ; + sh:path biolink:category ] ; sh:targetClass biolink:NoncodingRNAProduct . biolink:NucleicAcidSequenceMotif a sh:NodeShape ; sh:closed true ; sh:description "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ] ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ] ; sh:targetClass biolink:NucleicAcidSequenceMotif . biolink:NucleosomeModification a sh:NodeShape ; sh:closed true ; sh:description "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 9 ; sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 7 ; sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 6 ; + sh:path biolink:synonym ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 11 ; sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ] ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:NucleosomeModification . biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a observed expected frequency analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 10 ; sh:path biolink:category ], @@ -19150,20 +19172,20 @@ biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 7 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 2 ; @@ -19172,37 +19194,15 @@ biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 13 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ObservedExpectedFrequencyAnalysisResult . biolink:Occurrent a sh:NodeShape ; @@ -19215,32 +19215,39 @@ biolink:OrganismAttribute a sh:NodeShape ; sh:closed true ; sh:description "describes a characteristic of an organismal entity." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 5 ; + sh:path biolink:id ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; @@ -19249,9 +19256,6 @@ biolink:OrganismAttribute a sh:NodeShape ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -19259,29 +19263,25 @@ biolink:OrganismAttribute a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 0 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ] ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:OrganismAttribute . biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; @@ -19312,172 +19312,52 @@ biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:class biolink:NamedThing ; - sh:description "the environment in which the organism occurs" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:description "predicate describing the relationship between the taxon and the environment" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:NamedThing ; + sh:description "the environment in which the organism occurs" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OrganismTaxon ; sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; @@ -19485,333 +19365,351 @@ biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ] ; - sh:targetClass biolink:OrganismTaxonToEnvironmentAssociation . - -biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; - sh:closed false ; - sh:description "A relationship between two organism taxon nodes" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "predicate describing the relationship between the taxon and the environment" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; sh:path biolink:subject_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "organism taxon that is the subject of the association" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 35 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 17 ; + sh:path biolink:subject_category ] ; + sh:targetClass biolink:OrganismTaxonToEnvironmentAssociation . + +biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; + sh:closed false ; + sh:description "A relationship between two organism taxon nodes" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "a human-readable description of an entity" ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonAssociation . - -biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path rdf:subject ], + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "the environment in which the two taxa interact" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:associated_environmental_context ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + sh:path biolink:p_value ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OrganismTaxon ; + sh:description "organism taxon that is the subject of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:order 34 ; - sh:path rdf:type ], + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; + sh:order 12 ; sh:path biolink:agent_type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonAssociation . + +biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 17 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -19819,199 +19717,224 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:negated ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "the environment in which the two taxa interact" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:associated_environmental_context ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:order 36 ; + sh:path dct:description ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OrganismTaxon ; sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonInteraction . - -biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; - sh:closed true ; - sh:description "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the more general taxon" ; + sh:path biolink:has_attribute ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ], + sh:path rdf:predicate ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 7 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:OrganismTaxon ; + sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; + sh:order 8 ; sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:p_value ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonInteraction . + +biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; + sh:closed true ; + sh:description "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "the more specific taxon" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 31 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; @@ -20022,97 +19945,80 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the more specific taxon" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 32 ; - sh:path biolink:category ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . - -biolink:OrganismToOrganismAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:IndividualOrganism ; - sh:description "An association between two individual organisms." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -20120,100 +20026,121 @@ biolink:OrganismToOrganismAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 30 ; sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the more general taxon" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 35 ; + sh:path dct:description ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . + +biolink:OrganismToOrganismAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:order 32 ; sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:IndividualOrganism ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -20221,18 +20148,6 @@ biolink:OrganismToOrganismAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; @@ -20242,198 +20157,202 @@ biolink:OrganismToOrganismAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:IndividualOrganism ; + sh:description "An association between two individual organisms." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ] ; - sh:targetClass biolink:OrganismToOrganismAssociation . - -biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:qualified_predicate ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 15 ; + sh:path biolink:original_predicate ] ; + sh:targetClass biolink:OrganismToOrganismAssociation . + +biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:description "The relationship to the disease" ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 41 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:class biolink:OrganismalEntity ; sh:description "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease." ; sh:maxCount 1 ; @@ -20441,18 +20360,6 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; @@ -20462,34 +20369,60 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 35 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:subject_aspect_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:object_aspect_qualifier ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -20497,56 +20430,34 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ] ; - sh:targetClass biolink:OrganismalEntityAsAModelOfDiseaseAssociation . - -biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 40 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 38 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -20554,123 +20465,110 @@ biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "interaction relationship type" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "The relationship to the disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ] ; + sh:targetClass biolink:OrganismalEntityAsAModelOfDiseaseAssociation . + +biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "interaction relationship type" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -20678,111 +20576,137 @@ biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ] ; - sh:targetClass biolink:PairwiseGeneToGeneInteraction . - -biolink:PairwiseMolecularInteraction a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction at the molecular level between two physical entities" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; + sh:order 20 ; sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 36 ; + sh:order 35 ; sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; + sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:order 34 ; - sh:path rdf:type ], + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 14 ; + sh:order 13 ; sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 32 ; + sh:order 31 ; sh:path biolink:iri ], - [ sh:class biolink:MolecularEntity ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:GeneOrGeneProduct ; sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; + sh:order 28 ; + sh:path biolink:p_value ] ; + sh:targetClass biolink:PairwiseGeneToGeneInteraction . + +biolink:PairwiseMolecularInteraction a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction at the molecular level between two physical entities" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; @@ -20795,183 +20719,206 @@ biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:description "interaction relationship type" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:MolecularEntity ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:MolecularEntity ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + sh:order 3 ; + sh:path rdf:object ], + [ sh:description "interaction relationship type" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:order 0 ; + sh:path biolink:interacting_molecules_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:interacting_molecules_category ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; - sh:path biolink:original_predicate ] ; - sh:targetClass biolink:PairwiseMolecularInteraction . - -biolink:Patent a sh:NodeShape ; - sh:closed true ; - sh:description "a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:format ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:MolecularEntity ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:knowledge_source ] ; + sh:targetClass biolink:PairwiseMolecularInteraction . + +biolink:Patent a sh:NodeShape ; + sh:closed true ; + sh:description "a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 13 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:id ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:license ], [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:order 6 ; sh:path dct:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 8 ; @@ -20980,19 +20927,72 @@ biolink:Patent a sh:NodeShape ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:summary ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:has_attribute ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], + sh:order 9 ; + sh:path biolink:format ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:creation_date ], [ sh:description "mesh terms tagging a publication" ; sh:order 4 ; - sh:path biolink:mesh_terms ] ; + sh:path biolink:mesh_terms ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path rdfs:label ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:order 17 ; + sh:path rdf:type ] ; sh:targetClass biolink:Patent . biolink:PathognomonicityQuantifier a sh:NodeShape ; @@ -21005,12 +21005,43 @@ biolink:PathologicalAnatomicalExposure a sh:NodeShape ; sh:closed true ; sh:description "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -21025,57 +21056,26 @@ biolink:PathologicalAnatomicalExposure a sh:NodeShape ; [ sh:datatype xsd:string ; sh:order 12 ; sh:path rdf:type ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 10 ; sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ] ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ] ; sh:targetClass biolink:PathologicalAnatomicalExposure . biolink:PathologicalAnatomicalOutcome a sh:NodeShape ; @@ -21088,11 +21088,14 @@ biolink:PathologicalAnatomicalStructure a sh:NodeShape ; sh:closed true ; sh:description "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; sh:path biolink:synonym ], @@ -21101,51 +21104,48 @@ biolink:PathologicalAnatomicalStructure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; - sh:path biolink:category ] ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ] ; sh:targetClass biolink:PathologicalAnatomicalStructure . biolink:PathologicalEntityMixin a sh:NodeShape ; @@ -21158,21 +21158,45 @@ biolink:PathologicalProcess a sh:NodeShape ; sh:closed true ; sh:description "A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 14 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:iri ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path rdfs:label ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; @@ -21183,74 +21207,58 @@ biolink:PathologicalProcess a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:enabled_by ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], + sh:order 12 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:in_taxon_label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ] ; + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:PathologicalProcess . biolink:PathologicalProcessExposure a sh:NodeShape ; sh:closed true ; sh:description "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:full_name ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -21258,56 +21266,48 @@ biolink:PathologicalProcessExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path dct:description ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:order 12 ; sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 7 ; sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:class biolink:QuantityValue ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ] ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ] ; sh:targetClass biolink:PathologicalProcessExposure . biolink:PathologicalProcessOutcome a sh:NodeShape ; @@ -21320,30 +21320,7 @@ biolink:Phenomenon a sh:NodeShape ; sh:closed true ; sh:description "a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; @@ -21356,9 +21333,28 @@ biolink:Phenomenon a sh:NodeShape ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:full_name ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 3 ; sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -21368,113 +21364,161 @@ biolink:Phenomenon a sh:NodeShape ; [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 6 ; - sh:path biolink:category ] ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ] ; sh:targetClass biolink:Phenomenon . biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 48 ; sh:path biolink:frequency_qualifier ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 46 ; sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:double ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 36 ; + sh:path dct:description ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:order 40 ; sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 44 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -21485,46 +21529,23 @@ biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 17 ; sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -21532,140 +21553,87 @@ biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 43 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_percentage ], + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:subject_closure ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:has_count ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:description "a point in time" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ] ; + sh:order 5 ; + sh:path biolink:qualifier ] ; sh:targetClass biolink:PhenotypicFeatureToDiseaseAssociation . biolink:PhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:double ; + sh:property [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:qualified_predicate ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:has_total ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path rdf:subject ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:has_percentage ], + sh:order 10 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; @@ -21676,6 +21644,23 @@ biolink:PhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path rdf:subject ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -21683,148 +21668,157 @@ biolink:PhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:object_aspect_qualifier ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:sex_qualifier ] ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:qualified_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:subject_direction_qualifier ] ; sh:targetClass biolink:PhenotypicFeatureToEntityAssociationMixin . biolink:PhenotypicQuality a sh:NodeShape ; sh:closed true ; sh:description "A property of a phenotype" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; sh:path dct:description ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:order 11 ; sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ] ; + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:PhenotypicQuality . biolink:PhenotypicSex a sh:NodeShape ; sh:closed true ; sh:description "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 0 ; sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; sh:path dct:description ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -21834,12 +21828,18 @@ biolink:PhenotypicSex a sh:NodeShape ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ] ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:PhenotypicSex . biolink:PhysicalEssence a sh:NodeShape ; @@ -21857,61 +21857,61 @@ biolink:PhysicalEssenceOrOccurrent a sh:NodeShape ; biolink:PhysiologicalProcess a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:in_taxon_label ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; sh:path biolink:synonym ], @@ -21922,11 +21922,11 @@ biolink:PhysiologicalProcess a sh:NodeShape ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:order 12 ; sh:path rdf:type ] ; @@ -21936,39 +21936,27 @@ biolink:PlanetaryEntity a sh:NodeShape ; sh:closed true ; sh:description "Any entity or process that exists at the level of the whole planet" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -21977,49 +21965,54 @@ biolink:PlanetaryEntity a sh:NodeShape ; [ sh:description "Alternate human-readable names for a thing" ; sh:order 3 ; sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ] ; + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ] ; sh:targetClass biolink:PlanetaryEntity . biolink:Plant a sh:NodeShape ; sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; @@ -22030,46 +22023,24 @@ biolink:Plant a sh:NodeShape ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:Plant . - -biolink:Polypeptide a sh:NodeShape ; - sh:closed true ; - sh:description "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], @@ -22077,42 +22048,71 @@ biolink:Polypeptide a sh:NodeShape ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:in_taxon ], + sh:path biolink:in_taxon ] ; + sh:targetClass biolink:Plant . + +biolink:Polypeptide a sh:NodeShape ; + sh:closed true ; + sh:description "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ] ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Polypeptide . biolink:PopulationToPopulationAssociation a sh:NodeShape ; @@ -22126,308 +22126,281 @@ biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 30 ; sh:path biolink:id ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that form the object of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; sh:path biolink:subject_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that form the subject of the association" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 31 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that form the subject of the association" ; + sh:description "the population that form the object of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ] ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ] ; sh:targetClass biolink:PopulationToPopulationAssociation . biolink:PosttranslationalModification a sh:NodeShape ; sh:closed true ; sh:description "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ] ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ] ; sh:targetClass biolink:PosttranslationalModification . biolink:PreprintPublication a sh:NodeShape ; sh:closed true ; sh:description "a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:format ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:order 17 ; + sh:path rdf:type ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], + sh:order 18 ; + sh:path rdfs:label ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 19 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:order 6 ; + sh:path dct:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; @@ -22435,117 +22408,147 @@ biolink:PreprintPublication a sh:NodeShape ; sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:license ], + sh:order 8 ; + sh:path biolink:rights ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:has_attribute ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 6 ; - sh:path dct:type ], + sh:order 15 ; + sh:path biolink:iri ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 13 ; sh:path biolink:synonym ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:license ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 16 ; - sh:path biolink:category ] ; - sh:targetClass biolink:PreprintPublication . - -biolink:ProcessedMaterial a sh:NodeShape ; - sh:closed true ; - sh:description "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:deprecated ], + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 11 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:order 14 ; + sh:path biolink:id ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], + sh:order 0 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; - sh:description "" ; sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:format ], + [ sh:description "mesh terms tagging a publication" ; sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; + sh:order 2 ; + sh:path biolink:summary ] ; + sh:targetClass biolink:PreprintPublication . + +biolink:ProcessedMaterial a sh:NodeShape ; + sh:closed true ; + sh:description "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:iri ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 5 ; sh:path biolink:available_from ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:string ; + sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], [ sh:datatype xsd:string ; sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:is_toxic ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 12 ; + sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path dct:description ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; @@ -22555,18 +22558,15 @@ biolink:ProcessedMaterial a sh:NodeShape ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 12 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], + sh:order 17 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:description "" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ] ; + sh:order 4 ; + sh:path biolink:trade_name ] ; sh:targetClass biolink:ProcessedMaterial . biolink:Protein a sh:NodeShape ; @@ -22574,155 +22574,155 @@ biolink:Protein a sh:NodeShape ; sh:description "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ] ; + sh:order 3 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:Protein . biolink:ProteinDomain a sh:NodeShape ; sh:closed true ; sh:description "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 12 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 3 ; sh:path biolink:provided_by ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:id ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 9 ; sh:path biolink:category ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 6 ; sh:path biolink:synonym ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 4 ; sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], + sh:order 11 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:ProteinDomain . biolink:ProteinFamily a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; sh:order 6 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:iri ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -22732,193 +22732,190 @@ biolink:ProteinFamily a sh:NodeShape ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:in_taxon_label ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:deprecated ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:id ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 4 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ] ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ] ; sh:targetClass biolink:ProteinFamily . biolink:ProteinIsoform a sh:NodeShape ; sh:closed true ; sh:description "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ] ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:ProteinIsoform . biolink:RNAProduct a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:order 9 ; + sh:path rdf:type ], [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ] ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:RNAProduct . biolink:RNAProductIsoform a sh:NodeShape ; sh:closed true ; sh:description "Represents a protein that is a specific isoform of the canonical or reference RNA" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 3 ; @@ -22927,58 +22924,83 @@ biolink:RNAProductIsoform a sh:NodeShape ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 0 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:RNAProductIsoform . + +biolink:ReactionToCatalystAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:RNAProductIsoform . - -biolink:ReactionToCatalystAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], + sh:order 34 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], + sh:order 19 ; + sh:path biolink:original_object ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -22986,99 +23008,74 @@ biolink:ReactionToCatalystAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:description "the side of a reaction being modeled (ie: left or right)" ; - sh:in ( "left" "right" ) ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:reaction_side ], + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:order 33 ; + sh:path biolink:id ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:qualifiers ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; + sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:reaction_direction ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:MolecularEntity ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], + sh:order 3 ; + sh:path rdf:subject ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], + sh:order 40 ; + sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 35 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; - sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:reaction_direction ], + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; @@ -23086,114 +23083,158 @@ biolink:ReactionToCatalystAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 5 ; sh:path rdf:object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], + sh:order 17 ; + sh:path biolink:original_subject ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 39 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:integer ; + sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:stoichiometry ], + [ sh:description "the side of a reaction being modeled (ie: left or right)" ; + sh:in ( "left" "right" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:reaction_side ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:class biolink:MolecularEntity ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:subject ], + sh:order 20 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path rdf:predicate ] ; + sh:targetClass biolink:ReactionToCatalystAssociation . + +biolink:ReactionToParticipantAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path rdf:predicate ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path rdf:predicate ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ], + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 32 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:integer ; - sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:stoichiometry ] ; - sh:targetClass biolink:ReactionToCatalystAssociation . - -biolink:ReactionToParticipantAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 19 ; sh:path biolink:original_object ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], [ sh:class biolink:ChemicalEntity ; sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; @@ -23202,242 +23243,201 @@ biolink:ReactionToParticipantAssociation a sh:NodeShape ; sh:order 5 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; - sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:reaction_direction ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:class biolink:MolecularEntity ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], + sh:order 3 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:order 27 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:description "a point in time" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:order 37 ; + sh:path rdfs:label ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 35 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 40 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:integer ; + sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 0 ; + sh:path biolink:stoichiometry ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:description "the side of a reaction being modeled (ie: left or right)" ; - sh:in ( "left" "right" ) ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:reaction_side ], + sh:order 38 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], + sh:order 34 ; + sh:path biolink:iri ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:MolecularEntity ; - sh:description "the chemical entity or entity that is an interactor" ; + [ sh:description "the side of a reaction being modeled (ie: left or right)" ; + sh:in ( "left" "right" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], + sh:order 2 ; + sh:path biolink:reaction_side ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; + sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:integer ; - sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; + sh:order 1 ; + sh:path biolink:reaction_direction ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:stoichiometry ], + sh:order 6 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], + sh:minCount 1 ; + sh:order 33 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ] ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:subject_namespace ] ; sh:targetClass biolink:ReactionToParticipantAssociation . biolink:ReagentTargetedGene a sh:NodeShape ; sh:closed true ; sh:description "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; sh:order 7 ; sh:path biolink:synonym ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:in_taxon_label ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:id ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 9 ; sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 8 ; + sh:path biolink:iri ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:order 10 ; sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -23449,38 +23449,14 @@ biolink:RegulatoryRegion a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -23490,298 +23466,156 @@ biolink:RegulatoryRegion a sh:NodeShape ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:in_taxon ] ; - sh:targetClass biolink:RegulatoryRegion . - -biolink:RelationshipQuantifier a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:RelationshipQuantifier . - -biolink:RelationshipType a sh:NodeShape ; - sh:closed true ; - sh:description "An OWL property used as an edge label" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ] ; - sh:targetClass biolink:RelationshipType . - -biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; - sh:closed true ; - sh:description "A result of a relative frequency analysis." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:path biolink:in_taxon ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:order 11 ; + sh:order 10 ; sh:path rdf:type ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 12 ; + sh:order 11 ; sh:path rdfs:label ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 13 ; + sh:order 12 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:RelativeFrequencyAnalysisResult . + sh:order 1 ; + sh:path biolink:id ] ; + sh:targetClass biolink:RegulatoryRegion . -biolink:SensitivityQuantifier a sh:NodeShape ; +biolink:RelationshipQuantifier a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:SensitivityQuantifier . + sh:targetClass biolink:RelationshipQuantifier . -biolink:SequenceAssociation a sh:NodeShape ; +biolink:RelationshipType a sh:NodeShape ; sh:closed true ; - sh:description "An association between a sequence feature and a nucleic acid entity it is localized to." ; + sh:description "An OWL property used as an edge label" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 0 ; + sh:path biolink:id ] ; + sh:targetClass biolink:RelationshipType . + +biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; + sh:closed true ; + sh:description "A result of a relative frequency analysis." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 37 ; + sh:order 15 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; - sh:path biolink:qualifiers ], + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 3 ; - sh:path biolink:negated ], + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 10 ; + sh:path biolink:category ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 35 ; + sh:order 13 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 36 ; + sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 6 ; + sh:path biolink:full_name ] ; + sh:targetClass biolink:RelativeFrequencyAnalysisResult . + +biolink:SensitivityQuantifier a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:SensitivityQuantifier . + +biolink:SequenceAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a sequence feature and a nucleic acid entity it is localized to." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; @@ -23791,198 +23625,222 @@ biolink:SequenceAssociation a sh:NodeShape ; sh:order 13 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ] ; - sh:targetClass biolink:SequenceAssociation . - -biolink:SequenceFeatureRelationship a sh:NodeShape ; - sh:closed true ; - sh:description "For example, a particular exon is part of a particular transcript or gene" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:NucleicAcidEntity ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 28 ; + sh:path biolink:p_value ] ; + sh:targetClass biolink:SequenceAssociation . + +biolink:SequenceFeatureRelationship a sh:NodeShape ; + sh:closed true ; + sh:description "For example, a particular exon is part of a particular transcript or gene" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "a human-readable description of an entity" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -23990,38 +23848,14 @@ biolink:SequenceFeatureRelationship a sh:NodeShape ; sh:path biolink:subject_namespace ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ] ; - sh:targetClass biolink:SequenceFeatureRelationship . - -biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; - sh:closed false ; - sh:description "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -24029,36 +23863,103 @@ biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 31 ; sh:path biolink:iri ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -24066,68 +23967,111 @@ biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ] ; + sh:targetClass biolink:SequenceFeatureRelationship . + +biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; + sh:closed false ; + sh:description "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Treatment ; - sh:description "treatment whose efficacy is modulated by the subject variant" ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "a human-readable description of an entity" ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:SequenceVariant ; sh:description "variant that modulates the treatment of some disease" ; sh:maxCount 1 ; @@ -24135,172 +24079,228 @@ biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:class biolink:Treatment ; + sh:description "treatment whose efficacy is modulated by the subject variant" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; - sh:path biolink:qualifier ] ; + sh:path biolink:qualifier ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ] ; sh:targetClass biolink:SequenceVariantModulatesTreatmentAssociation . biolink:Serial a sh:NodeShape ; sh:closed true ; sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:issue ], + sh:order 15 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:license ], + sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; + sh:order 20 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:iso_abbreviation ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 16 ; - sh:path biolink:synonym ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 7 ; - sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:order 4 ; sh:path biolink:pages ], [ sh:datatype xsd:string ; - sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; - sh:order 20 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:volume ], [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:order 9 ; sh:path dct:type ], - [ sh:datatype xsd:string ; - sh:description "Serials (journals) should have industry-standard identifier such as from ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:id ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:creation_date ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:summary ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; sh:order 6 ; sh:path biolink:keywords ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:format ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:issue ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 16 ; + sh:path biolink:synonym ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 7 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:deprecated ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 18 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:volume ], - [ sh:description "a long-form human readable name for a thing" ; + sh:order 12 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 14 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 5 ; + sh:path biolink:summary ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_attribute ], + sh:order 22 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Serials (journals) should have industry-standard identifier such as from ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:authors ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 14 ; - sh:path biolink:provided_by ] ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:creation_date ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Serial . biolink:SeverityValue a sh:NodeShape ; @@ -24311,214 +24311,214 @@ biolink:SeverityValue a sh:NodeShape ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 0 ; sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:QuantityValue ; + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ] ; + sh:order 13 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:SeverityValue . biolink:SiRNA a sh:NodeShape ; sh:closed true ; sh:description "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ] ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ] ; sh:targetClass biolink:SiRNA . biolink:SmallMolecule a sh:NodeShape ; sh:closed true ; sh:description "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 2 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:boolean ; - sh:description "indicates whether a molecular entity is a metabolite" ; + sh:order 17 ; + sh:path biolink:deprecated ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_metabolite ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:order 13 ; - sh:path rdf:type ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:id ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:max_tolerated_dose ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:id ], + sh:order 15 ; + sh:path dct:description ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 2 ; + sh:path biolink:available_from ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:is_toxic ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:trade_name ], + [ sh:datatype xsd:boolean ; + sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:is_metabolite ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path rdfs:label ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; sh:path biolink:synonym ] ; @@ -24528,121 +24528,105 @@ biolink:Snv a sh:NodeShape ; sh:closed true ; sh:description "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:class biolink:Gene ; - sh:description "Each allele can be associated with any number of genes" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene ], + sh:order 4 ; + sh:path biolink:in_taxon_label ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 12 ; sh:path rdfs:label ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], [ sh:description "The state of the sequence w.r.t a reference sequence" ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:has_biological_sequence ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ] ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:class biolink:Gene ; + sh:description "Each allele can be associated with any number of genes" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Snv . biolink:SocioeconomicExposure a sh:NodeShape ; sh:closed true ; sh:description "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; sh:order 12 ; sh:path rdf:type ], - [ sh:class biolink:NamedThing ; + [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -24650,17 +24634,9 @@ biolink:SocioeconomicExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:SocioeconomicAttribute ; - sh:description "connects any entity to an attribute" ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 1 ; @@ -24669,10 +24645,34 @@ biolink:SocioeconomicExposure a sh:NodeShape ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:timepoint ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:full_name ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:class biolink:SocioeconomicAttribute ; + sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ] ; sh:targetClass biolink:SocioeconomicExposure . biolink:SocioeconomicOutcome a sh:NodeShape ; @@ -24690,55 +24690,55 @@ biolink:Study a sh:NodeShape ; sh:closed true ; sh:description "a detailed investigation and/or analysis" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ] ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ] ; sh:targetClass biolink:Study . biolink:StudyPopulation a sh:NodeShape ; @@ -24748,89 +24748,68 @@ biolink:StudyPopulation a sh:NodeShape ; sh:property [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:in_taxon ] ; - sh:targetClass biolink:StudyPopulation . - -biolink:StudyResult a sh:NodeShape ; - sh:closed false ; - sh:description "A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:path biolink:in_taxon ], [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; + sh:targetClass biolink:StudyPopulation . + +biolink:StudyResult a sh:NodeShape ; + sh:closed false ; + sh:description "A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:full_name ], @@ -24840,113 +24819,134 @@ biolink:StudyResult a sh:NodeShape ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:format ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 7 ; sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ] ; + sh:order 13 ; + sh:path dct:description ] ; sh:targetClass biolink:StudyResult . biolink:StudyVariable a sh:NodeShape ; sh:closed true ; sh:description "a variable that is used as a measure in the investigation of a study" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:rights ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ] ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:StudyVariable . biolink:SubjectOfInvestigation a sh:NodeShape ; @@ -24958,158 +24958,164 @@ biolink:SubjectOfInvestigation a sh:NodeShape ; biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "An association between individuals of different taxa." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 35 ; + sh:path dct:description ], [ sh:class biolink:OrganismTaxon ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "An association between individuals of different taxa." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -25117,50 +25123,70 @@ biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:order 18 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "a human-readable description of an entity" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; - sh:path biolink:subject_namespace ] ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ] ; sh:targetClass biolink:TaxonToTaxonAssociation . biolink:TextMiningResult a sh:NodeShape ; sh:closed true ; sh:description "A result of text mining." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:order 2 ; + sh:path biolink:format ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; sh:path dct:description ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -25176,118 +25202,89 @@ biolink:TextMiningResult a sh:NodeShape ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ] ; + sh:path biolink:rights ] ; sh:targetClass biolink:TextMiningResult . biolink:ThingWithTaxon a sh:NodeShape ; sh:closed false ; sh:description "A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; - sh:path biolink:in_taxon_label ] ; - sh:targetClass biolink:ThingWithTaxon . - -biolink:TranscriptToGeneRelationship a sh:NodeShape ; - sh:closed true ; - sh:description "A gene is a collection of transcripts" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; + sh:targetClass biolink:ThingWithTaxon . + +biolink:TranscriptToGeneRelationship a sh:NodeShape ; + sh:closed true ; + sh:description "A gene is a collection of transcripts" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; @@ -25299,36 +25296,63 @@ biolink:TranscriptToGeneRelationship a sh:NodeShape ; sh:minCount 1 ; sh:order 30 ; sh:path biolink:id ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Transcript ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:class biolink:Gene ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -25336,244 +25360,256 @@ biolink:TranscriptToGeneRelationship a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; sh:path rdf:type ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a point in time" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Transcript ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ] ; - sh:targetClass biolink:TranscriptToGeneRelationship . - -biolink:TranscriptionFactorBindingSite a sh:NodeShape ; - sh:closed true ; - sh:description "A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; + sh:order 35 ; sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; sh:order 9 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:path biolink:primary_knowledge_source ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 31 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:TranscriptToGeneRelationship . + +biolink:TranscriptionFactorBindingSite a sh:NodeShape ; + sh:closed true ; + sh:description "A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ] ; sh:targetClass biolink:TranscriptionFactorBindingSite . biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:SequenceVariant ; + sh:description "A variant that has a role in modeling the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:frequency_qualifier ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "The relationship to the disease" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -25581,148 +25617,136 @@ biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; sh:path rdfs:label ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "The relationship to the disease" ; + sh:order 42 ; + sh:path biolink:qualified_predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_direction_qualifier ], + sh:order 43 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:SequenceVariant ; - sh:description "A variant that has a role in modeling the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 35 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:qualified_predicate ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ] ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ] ; sh:targetClass biolink:VariantAsAModelOfDiseaseAssociation . biolink:VariantToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:property [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 39 ; @@ -25732,431 +25756,407 @@ biolink:VariantToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "E.g. is pathogenic for" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:class biolink:Disease ; + sh:description "a disease that is associated with that variant" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; + sh:order 35 ; + sh:path dct:description ], + [ sh:description "E.g. is pathogenic for" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_direction_qualifier ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Disease ; - sh:description "a disease that is associated with that variant" ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 40 ; sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:order 42 ; sh:path biolink:qualified_predicate ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ] ; + sh:order 17 ; + sh:path biolink:subject_category ] ; sh:targetClass biolink:VariantToDiseaseAssociation . biolink:VariantToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated with some other entity" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:VariantToEntityAssociationMixin . biolink:VariantToGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 32 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "a point in time" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "a human-readable description of an entity" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:qualifier ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated with some other entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ] ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ] ; sh:targetClass biolink:VariantToGeneAssociation . biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; @@ -26164,45 +26164,11 @@ biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; sh:description "An association between a variant and expression of a gene (i.e. e-QTL)" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; + sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -26210,243 +26176,221 @@ biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 16 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:label ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated with some other entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 34 ; - sh:path biolink:id ], + sh:order 35 ; + sh:path biolink:iri ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:phenotypic_state ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:order 40 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 14 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path rdf:predicate ], + sh:order 18 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; - sh:path biolink:category ], + sh:order 1 ; + sh:path biolink:expression_site ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 37 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:timepoint ], + sh:order 10 ; + sh:path biolink:publications ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:order 33 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], - [ sh:description "a human-readable description of an entity" ; + sh:order 4 ; + sh:path rdf:subject ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 36 ; + sh:path biolink:category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 19 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:stage_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:minCount 1 ; + sh:order 34 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path rdfs:label ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ], + sh:order 6 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:phenotypic_state ], + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_subject ] ; - sh:targetClass biolink:VariantToGeneExpressionAssociation . - -biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 20 ; + sh:path biolink:original_object ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 10 ; + sh:order 13 ; sh:path biolink:primary_knowledge_source ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 36 ; + sh:order 39 ; sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:minCount 1 ; + sh:order 5 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; + sh:order 17 ; + sh:path biolink:timepoint ] ; + sh:targetClass biolink:VariantToGeneExpressionAssociation . + +biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -26454,31 +26398,47 @@ biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], + sh:order 43 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -26486,216 +26446,262 @@ biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 47 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 38 ; sh:path biolink:deprecated ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:order 41 ; sh:path biolink:has_quotient ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:order 42 ; sh:path biolink:has_percentage ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], + sh:order 44 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:order 40 ; sh:path biolink:has_total ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 39 ; + sh:path biolink:has_count ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:subject_aspect_qualifier ] ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ] ; sh:targetClass biolink:VariantToPhenotypicFeatureAssociation . biolink:VariantToPopulationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a variant and a population, where the variant has particular frequency in the population" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 35 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:original_object ], + sh:order 33 ; + sh:path biolink:p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 41 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 37 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:class biolink:SequenceVariant ; - sh:description "an allele that has a certain frequency in a given population" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 42 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:integer ; + sh:description "number all populations that carry a particular allele, aka allele number" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 4 ; + sh:path biolink:has_total ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path rdfs:label ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 18 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 38 ; - sh:path rdf:type ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 37 ; + sh:path biolink:category ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -26703,73 +26709,95 @@ biolink:VariantToPopulationAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 17 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 13 ; + sh:path biolink:knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:has_percentage ], + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:subject_namespace ], + sh:order 19 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:double ; + sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 15 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 21 ; + sh:path biolink:original_object ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:frequency_qualifier ], + sh:order 40 ; + sh:path dct:description ], + [ sh:class biolink:SequenceVariant ; + sh:description "an allele that has a certain frequency in a given population" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 9 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 38 ; + sh:path rdf:type ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], + sh:order 11 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:double ; - sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:has_quotient ], + sh:order 28 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:PopulationOfIndividualOrganisms ; sh:description "the population that is observed to have the frequency" ; sh:maxCount 1 ; @@ -26777,89 +26805,51 @@ biolink:VariantToPopulationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:datatype xsd:integer ; - sh:description "number all populations that carry a particular allele, aka allele number" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:has_total ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 23 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 6 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_source ], + sh:order 34 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:integer ; sh:description "number in object population that carry a particular allele, aka allele count" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 10 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_subject ] ; + sh:order 8 ; + sh:path biolink:negated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:iri ] ; sh:targetClass biolink:VariantToPopulationAssociation . biolink:Vertebrate a sh:NodeShape ; sh:closed true ; sh:description "A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 11 ; + sh:path dct:description ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; @@ -26869,281 +26859,291 @@ biolink:Vertebrate a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ] ; - sh:targetClass biolink:Vertebrate . - -biolink:Virus a sh:NodeShape ; - sh:closed true ; - sh:description "A virus is a microorganism that replicates itself as a microRNA and infects the host cell." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ] ; + sh:targetClass biolink:Vertebrate . + +biolink:Virus a sh:NodeShape ; + sh:closed true ; + sh:description "A virus is a microorganism that replicates itself as a microRNA and infects the host cell." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; sh:path biolink:synonym ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 9 ; + sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ] ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ] ; sh:targetClass biolink:Virus . biolink:WebPage a sh:NodeShape ; sh:closed true ; sh:description "a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:description "mesh terms tagging a publication" ; + sh:property [ sh:description "mesh terms tagging a publication" ; sh:order 4 ; sh:path biolink:mesh_terms ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:authors ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:summary ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 6 ; - sh:path dct:type ], + sh:order 15 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 11 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:format ], + sh:order 19 ; + sh:path dct:description ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:order 6 ; + sh:path dct:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:category ], [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:order 18 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + sh:order 12 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:order 17 ; - sh:path rdf:type ], + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:license ], [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:rights ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:order 17 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:creation_date ] ; + sh:order 9 ; + sh:path biolink:format ] ; sh:targetClass biolink:WebPage . biolink:Behavior a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; sh:path biolink:id ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path dct:description ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], + sh:order 1 ; + sh:path biolink:has_input ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 2 ; + sh:path biolink:has_output ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:order 12 ; sh:path rdf:type ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ] ; + sh:order 13 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Behavior . biolink:BehavioralFeature a sh:NodeShape ; @@ -27154,60 +27154,60 @@ biolink:BehavioralFeature a sh:NodeShape ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:BehavioralFeature . biolink:BiologicalProcess a sh:NodeShape ; @@ -27215,165 +27215,166 @@ biolink:BiologicalProcess a sh:NodeShape ; sh:description "One or more causally connected executions of molecular functions" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:iri ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:in_taxon_label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 14 ; sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:enabled_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ] ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ] ; sh:targetClass biolink:BiologicalProcess . biolink:CellularComponent a sh:NodeShape ; sh:closed true ; sh:description "A location in or around a cell" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ] ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:CellularComponent . biolink:ClinicalAttribute a sh:NodeShape ; sh:closed true ; sh:description "Attributes relating to a clinical manifestation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; @@ -27388,6 +27389,9 @@ biolink:ClinicalAttribute a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -27395,82 +27399,53 @@ biolink:ClinicalAttribute a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ] ; + sh:order 10 ; + sh:path biolink:category ] ; sh:targetClass biolink:ClinicalAttribute . biolink:Dataset a sh:NodeShape ; sh:closed true ; sh:description "an item that refers to a collection of data from a data source." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:format ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 12 ; sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; @@ -27480,187 +27455,200 @@ biolink:Dataset a sh:NodeShape ; sh:maxCount 1 ; sh:order 13 ; sh:path dct:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ] ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ] ; sh:targetClass biolink:Dataset . biolink:DatasetDistribution a sh:NodeShape ; sh:closed true ; sh:description "an item that holds distribution level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:creation_date ], + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:distribution_download_url ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 6 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:full_name ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:distribution_download_url ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 9 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 13 ; sh:path rdfs:label ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:format ], + sh:order 1 ; + sh:path biolink:license ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:license ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 8 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 16 ; - sh:path biolink:deprecated ] ; + sh:path biolink:deprecated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:format ] ; sh:targetClass biolink:DatasetDistribution . biolink:Device a sh:NodeShape ; sh:closed true ; sh:description "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:order 7 ; sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ] ; sh:targetClass biolink:Device . biolink:Exon a sh:NodeShape ; sh:closed true ; sh:description "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; sh:path biolink:synonym ], @@ -27669,28 +27657,40 @@ biolink:Exon a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ] ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ] ; sh:targetClass biolink:Exon . biolink:GeneFamily a sh:NodeShape ; @@ -27698,198 +27698,197 @@ biolink:GeneFamily a sh:NodeShape ; sh:description "any grouping of multiple genes or gene products related by common descent" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:id ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:in_taxon_label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path rdf:type ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ], + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:deprecated ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; sh:path dct:description ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ] ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:GeneFamily . biolink:GeneProductMixin a sh:NodeShape ; sh:closed false ; sh:description "The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path rdfs:label ], + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ] ; + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path rdfs:label ] ; sh:targetClass biolink:GeneProductMixin . biolink:GeneticInheritance a sh:NodeShape ; sh:closed true ; sh:description "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ] ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ] ; sh:targetClass biolink:GeneticInheritance . biolink:InformationContentEntity a sh:NodeShape ; sh:closed false ; sh:description "a piece of information that typically describes some topic of discourse or is used as support." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 12 ; + sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], + sh:order 0 ; + sh:path biolink:license ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; @@ -27899,28 +27898,42 @@ biolink:InformationContentEntity a sh:NodeShape ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:creation_date ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ] ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:InformationContentEntity . biolink:Onset a sh:NodeShape ; sh:closed true ; sh:description "The age group in which (disease) symptom manifestations appear." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -27930,10 +27943,28 @@ biolink:Onset a sh:NodeShape ; sh:minCount 1 ; sh:order 10 ; sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 0 ; @@ -27947,108 +27978,77 @@ biolink:Onset a sh:NodeShape ; [ sh:datatype xsd:string ; sh:order 11 ; sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ] ; + sh:order 1 ; + sh:path biolink:has_attribute_type ] ; sh:targetClass biolink:Onset . biolink:OrganismalEntity a sh:NodeShape ; sh:closed false ; sh:description "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ] ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:OrganismalEntity . biolink:PredicateMapping a sh:NodeShape ; @@ -28056,83 +28056,89 @@ biolink:PredicateMapping a sh:NodeShape ; sh:description "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 3 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:broad_match ], + [ sh:datatype xsd:string ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 16 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:subject_part_qualifier ], + sh:order 6 ; + sh:path biolink:subject_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:narrow_match ], + sh:order 0 ; + sh:path biolink:mapped_predicate ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:object_part_qualifier ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:subject_context_qualifier ], [ sh:class biolink:NamedThing ; sh:description "holds between two entities that have strictly equivalent meanings, with a high degree of confidence" ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:exact_match ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:qualified_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:subject_direction_qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; + sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:object_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:anatomical_context_qualifier ], + sh:order 5 ; + sh:path biolink:subject_derivative_qualifier ], [ sh:datatype xsd:string ; sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:object_form_or_variant_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:object_derivative_qualifier ], [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:causal_mechanism_qualifier ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_derivative_qualifier ], + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_form_or_variant_qualifier ], + sh:order 4 ; + sh:path biolink:subject_part_qualifier ], [ sh:class biolink:OrganismTaxon ; sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; @@ -28140,150 +28146,144 @@ biolink:PredicateMapping a sh:NodeShape ; sh:order 17 ; sh:path biolink:species_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:mapped_predicate ], + sh:order 14 ; + sh:path biolink:object_context_qualifier ], [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; + sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:broad_match ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 19 ; + sh:path biolink:narrow_match ], + [ sh:datatype xsd:string ; + sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path rdf:predicate ] ; + sh:order 13 ; + sh:path biolink:object_derivative_qualifier ] ; sh:targetClass biolink:PredicateMapping . biolink:Procedure a sh:NodeShape ; sh:closed true ; sh:description "A series of actions conducted in a certain order or manner" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 3 ; sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ] ; + sh:order 9 ; + sh:path dct:description ] ; sh:targetClass biolink:Procedure . biolink:SocioeconomicAttribute a sh:NodeShape ; sh:closed true ; sh:description "Attributes relating to a socioeconomic manifestation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path biolink:category ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; sh:path biolink:synonym ] ; @@ -28305,126 +28305,110 @@ biolink:Treatment a sh:NodeShape ; sh:closed true ; sh:description "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Procedure ; - sh:description "connects an entity to one or more (medical) procedures" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_procedure ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; sh:order 7 ; sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:timepoint ], + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:class biolink:Drug ; sh:description "connects an entity to one or more drugs" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_drug ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], [ sh:class biolink:Device ; sh:description "connects an entity to one or more (medical) devices" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_device ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:description "a point in time" ; sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Procedure ; + sh:description "connects an entity to one or more (medical) procedures" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_procedure ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ] ; + sh:order 10 ; + sh:path biolink:category ] ; sh:targetClass biolink:Treatment . biolink:Zygosity a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 12 ; + sh:path dct:description ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 0 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; @@ -28434,81 +28418,97 @@ biolink:Zygosity a sh:NodeShape ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:order 11 ; sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ] ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:Zygosity . biolink:Case a sh:NodeShape ; sh:closed true ; - sh:description "An individual (human) organism that has a patient role in some clinical context." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + sh:description "An individual (human) organism that has a patient role in some clinical context." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ] ; + sh:path rdfs:label ] ; sh:targetClass biolink:Case . biolink:CellLine a sh:NodeShape ; @@ -28519,37 +28519,48 @@ biolink:CellLine a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -28560,82 +28571,71 @@ biolink:CellLine a sh:NodeShape ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; - sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ] ; + sh:path biolink:id ] ; sh:targetClass biolink:CellLine . biolink:IndividualOrganism a sh:NodeShape ; sh:closed true ; sh:description "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ] ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ] ; sh:targetClass biolink:IndividualOrganism . biolink:Outcome a sh:NodeShape ; @@ -28648,18 +28648,15 @@ biolink:Transcript a sh:NodeShape ; sh:closed true ; sh:description "An RNA synthesized on a DNA or RNA template by an RNA polymerase." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], @@ -28667,143 +28664,146 @@ biolink:Transcript a sh:NodeShape ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ] ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Transcript . biolink:Drug a sh:NodeShape ; sh:closed true ; sh:description "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:is_supplement ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:is_toxic ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 11 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:full_name ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 4 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 6 ; - sh:path biolink:available_from ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:trade_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], + sh:order 17 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_chemical_role ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], + sh:order 15 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; - sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:description "" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:description "a human-readable description of an entity" ; + sh:order 1 ; + sh:path biolink:is_supplement ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ], + sh:order 20 ; + sh:path biolink:deprecated ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 14 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:trade_name ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_chemical_role ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 11 ; + sh:path biolink:xref ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 6 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:is_toxic ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 4 ; + sh:path biolink:routes_of_delivery ] ; sh:targetClass biolink:Drug . biolink:ExposureEvent a sh:NodeShape ; @@ -28827,33 +28827,27 @@ biolink:MaterialSample a sh:NodeShape ; sh:description "A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 2 ; @@ -28864,13 +28858,19 @@ biolink:MaterialSample a sh:NodeShape ; [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 9 ; sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; @@ -28880,38 +28880,7 @@ biolink:MaterialSample a sh:NodeShape ; biolink:Pathway a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; @@ -28921,38 +28890,69 @@ biolink:Pathway a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 0 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 13 ; sh:path rdfs:label ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ] ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:Pathway . biolink:LifeStage a sh:NodeShape ; @@ -28963,16 +28963,23 @@ biolink:LifeStage a sh:NodeShape ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], @@ -28980,25 +28987,6 @@ biolink:LifeStage a sh:NodeShape ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -29014,62 +29002,49 @@ biolink:LifeStage a sh:NodeShape ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ] ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:LifeStage . biolink:NucleicAcidEntity a sh:NodeShape ; sh:closed true ; sh:description "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 11 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:trade_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], + sh:order 20 ; + sh:path biolink:deprecated ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 13 ; sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; @@ -29079,41 +29054,66 @@ biolink:NucleicAcidEntity a sh:NodeShape ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 6 ; sh:path biolink:available_from ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:is_toxic ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:boolean ; sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:is_metabolite ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:is_toxic ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:order 16 ; + sh:path rdf:type ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 17 ; - sh:path rdfs:label ] ; + sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 11 ; + sh:path biolink:xref ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:trade_name ] ; sh:targetClass biolink:NucleicAcidEntity . biolink:MolecularActivity a sh:NodeShape ; @@ -29124,101 +29124,123 @@ biolink:MolecularActivity a sh:NodeShape ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 13 ; sh:path rdfs:label ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "The gene product, gene, or complex that catalyzes the reaction" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], [ sh:class biolink:MolecularEntity ; sh:description "A chemical entity that is the input for the reaction" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_input ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 5 ; + sh:path biolink:in_taxon_label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:iri ], [ sh:class biolink:MolecularEntity ; sh:description "A chemical entity that is the output for the reaction" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "The gene product, gene, or complex that catalyzes the reaction" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ] ; + sh:order 0 ; + sh:path biolink:id ] ; sh:targetClass biolink:MolecularActivity . biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; sh:closed true ; sh:description "A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; @@ -29227,36 +29249,14 @@ biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ] ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:PopulationOfIndividualOrganisms . biolink:MacromolecularMachineMixin a sh:NodeShape ; @@ -29273,17 +29273,13 @@ biolink:MolecularEntity a sh:NodeShape ; sh:closed true ; sh:description "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ], + sh:order 15 ; + sh:path dct:description ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 2 ; @@ -29293,119 +29289,123 @@ biolink:MolecularEntity a sh:NodeShape ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:is_toxic ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:max_tolerated_dose ], + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:trade_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "indicates whether a molecular entity is a metabolite" ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_metabolite ], + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 10 ; sh:path biolink:id ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_chemical_role ] ; + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:boolean ; + sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:is_metabolite ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ] ; sh:targetClass biolink:MolecularEntity . biolink:PhysicalEntity a sh:NodeShape ; sh:closed true ; sh:description "An entity that has material reality (a.k.a. physical essence)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; sh:order 7 ; sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ] ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:PhysicalEntity . biolink:ChemicalEntityOrGeneOrGeneProduct a sh:NodeShape ; @@ -29418,400 +29418,362 @@ biolink:Genotype a sh:NodeShape ; sh:closed true ; sh:description "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Zygosity ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_zygosity ], + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:order 7 ; + sh:path biolink:full_name ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:order 11 ; sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:description "connects a genomic feature to its sequence" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 13 ; + sh:path dct:description ], + [ sh:class biolink:Zygosity ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 0 ; + sh:path biolink:has_zygosity ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 4 ; + sh:path biolink:in_taxon_label ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 8 ; - sh:path biolink:synonym ] ; + sh:path biolink:synonym ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:has_biological_sequence ] ; sh:targetClass biolink:Genotype . biolink:PhenotypicFeature a sh:NodeShape ; sh:closed true ; sh:description "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ] ; + sh:path biolink:synonym ] ; sh:targetClass biolink:PhenotypicFeature . biolink:SequenceVariant a sh:NodeShape ; sh:closed true ; sh:description "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:in_taxon_label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 5 ; sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 6 ; sh:path biolink:xref ], + [ sh:class biolink:Gene ; + sh:description "Each allele can be associated with any number of genes" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:full_name ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], [ sh:description "The state of the sequence w.r.t a reference sequence" ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:has_biological_sequence ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:class biolink:Gene ; - sh:description "Each allele can be associated with any number of genes" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:order 11 ; - sh:path rdf:type ] ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ] ; sh:targetClass biolink:SequenceVariant . biolink:ChemicalEntity a sh:NodeShape ; sh:closed true ; sh:description "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_toxic ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:trade_name ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_chemical_role ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:id ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 13 ; sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:iri ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:category ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 8 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 7 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:ChemicalEntity . - -biolink:Agent a sh:NodeShape ; - sh:closed true ; - sh:description "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 14 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 15 ; sh:path biolink:has_attribute ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:address ], - [ sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; - sh:order 0 ; - sh:path biolink:affiliation ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:is_toxic ] ; + sh:targetClass biolink:ChemicalEntity . + +biolink:Agent a sh:NodeShape ; + sh:closed true ; + sh:description "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code." ; + sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path biolink:address ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:Agent . - -biolink:ChemicalRole a sh:NodeShape ; - sh:closed true ; - sh:description "A role played by the molecular entity or part thereof within a chemical context." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; + sh:order 11 ; sh:path dct:description ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; - sh:path biolink:provided_by ], + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; + sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 10 ; + sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; + sh:order 0 ; + sh:path biolink:affiliation ], + [ sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:Agent . + +biolink:ChemicalRole a sh:NodeShape ; + sh:closed true ; + sh:description "A role played by the molecular entity or part thereof within a chemical context." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -29824,6 +29786,13 @@ biolink:ChemicalRole a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; @@ -29833,25 +29802,56 @@ biolink:ChemicalRole a sh:NodeShape ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:deprecated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 0 ; - sh:path rdfs:label ] ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ] ; sh:targetClass biolink:ChemicalRole . biolink:DiseaseOrPhenotypicFeature a sh:NodeShape ; sh:closed true ; sh:description "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; @@ -29862,45 +29862,45 @@ biolink:DiseaseOrPhenotypicFeature a sh:NodeShape ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeature . biolink:Gene a sh:NodeShape ; @@ -29920,80 +29920,103 @@ biolink:Gene a sh:NodeShape ; sh:minCount 1 ; sh:order 10 ; sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:description "a long-form human readable name for a thing" ; + sh:order 13 ; + sh:path dct:description ], + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], + sh:order 2 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 12 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Symbol for a particular thing" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:symbol ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ] ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:Gene . biolink:BiologicalSex a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; @@ -30002,57 +30025,41 @@ biolink:BiologicalSex a sh:NodeShape ; sh:maxCount 1 ; sh:order 12 ; sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:order 11 ; sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:has_qualitative_value ] ; + sh:path biolink:has_qualitative_value ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:BiologicalSex . biolink:Disease a sh:NodeShape ; sh:closed true ; sh:description "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], @@ -30060,120 +30067,113 @@ biolink:Disease a sh:NodeShape ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ] ; + sh:order 9 ; + sh:path rdf:type ] ; sh:targetClass biolink:Disease . biolink:AnatomicalEntity a sh:NodeShape ; sh:closed true ; sh:description "A subcellular location, cell type or gross anatomical part" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ] ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ] ; sh:targetClass biolink:AnatomicalEntity . biolink:GeneOrGeneProduct a sh:NodeShape ; @@ -30190,41 +30190,62 @@ biolink:QuantityValue a sh:NodeShape ; sh:closed true ; sh:description "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:double ; + sh:property [ sh:description "connects a quantity value to a unit" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_unit ], + [ sh:datatype xsd:double ; sh:description "connects a quantity value to a number" ; sh:maxCount 1 ; sh:order 1 ; - sh:path biolink:has_numeric_value ], - [ sh:description "connects a quantity value to a unit" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_unit ] ; + sh:path biolink:has_numeric_value ] ; sh:targetClass biolink:QuantityValue . biolink:OrganismTaxon a sh:NodeShape ; sh:closed true ; sh:description "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:order 8 ; - sh:path rdf:type ], + sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:full_name ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], [ sh:class biolink:TaxonomicRank ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_taxonomic_rank ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:order 8 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:deprecated ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 4 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -30235,30 +30256,9 @@ biolink:OrganismTaxon a sh:NodeShape ; sh:maxCount 1 ; sh:order 9 ; sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:category ] ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 4 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:OrganismTaxon . biolink:EvidenceType a sh:NodeShape ; @@ -30269,13 +30269,21 @@ biolink:EvidenceType a sh:NodeShape ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -30283,64 +30291,59 @@ biolink:EvidenceType a sh:NodeShape ; sh:order 8 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ] ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:EvidenceType . biolink:NamedThing a sh:NodeShape ; sh:closed true ; sh:description "a databased entity or concept/class" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -30350,126 +30353,121 @@ biolink:NamedThing a sh:NodeShape ; [ sh:datatype xsd:string ; sh:order 7 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:NamedThing . biolink:Publication a sh:NodeShape ; sh:closed true ; sh:description "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + sh:order 15 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; sh:order 3 ; sh:path biolink:keywords ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:category ], + sh:order 10 ; + sh:path biolink:creation_date ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], [ sh:description "mesh terms tagging a publication" ; sh:order 4 ; sh:path biolink:mesh_terms ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:summary ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:order 6 ; + sh:path dct:type ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:creation_date ], + sh:order 12 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 6 ; - sh:path dct:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:license ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 13 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:format ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:order 19 ; + sh:path dct:description ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 16 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:order 17 ; sh:path rdf:type ], @@ -30480,97 +30478,99 @@ biolink:Publication a sh:NodeShape ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:rights ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ] ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:id ] ; sh:targetClass biolink:Publication . biolink:RetrievalSource a sh:NodeShape ; sh:closed true ; sh:description "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:license ], + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:resource_id ], + [ sh:datatype xsd:string ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 8 ; + sh:path biolink:provided_by ], [ sh:description "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." ; sh:in ( "primary_knowledge_source" "aggregator_knowledge_source" "supporting_data_source" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path biolink:resource_role ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:format ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ], [ sh:description "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:upstream_resource_ids ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:format ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:rights ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], - [ sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:resource_id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 8 ; - sh:path biolink:provided_by ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:creation_date ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ] ; + sh:order 16 ; + sh:path dct:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:license ] ; sh:targetClass biolink:RetrievalSource . biolink:Attribute a sh:NodeShape ; @@ -30578,39 +30578,39 @@ biolink:Attribute a sh:NodeShape ; sh:description "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -30618,32 +30618,32 @@ biolink:Attribute a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ] ; + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ] ; sh:targetClass biolink:Attribute . biolink:OntologyClass a sh:NodeShape ; diff --git a/src/biolink_model/datamodel/model.py b/src/biolink_model/datamodel/model.py index eec25b05b..eccd6f888 100644 --- a/src/biolink_model/datamodel/model.py +++ b/src/biolink_model/datamodel/model.py @@ -1,5 +1,5 @@ # Auto generated from biolink_model.yaml by pythongen.py version: 0.0.1 -# Generation date: 2024-05-10T23:03:26 +# Generation date: 2024-05-10T16:31:18 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model diff --git a/src/biolink_model/schema/biolink_model.yaml b/src/biolink_model/schema/biolink_model.yaml index 5003a3601..57b665cad 100644 --- a/src/biolink_model/schema/biolink_model.yaml +++ b/src/biolink_model/schema/biolink_model.yaml @@ -3403,7 +3403,7 @@ slots: promotes condition: mixin: true - is_a: related to at instance level + is_a: affects likelihood of description: >- Holds between a substance, procedure, or activity and a medical condition (disease or phenotypic feature), and states that the substance, procedure, or activity is able to promote it manifesting in the first place. @@ -3417,7 +3417,7 @@ slots: condition promoted by: mixin: true - is_a: related to at instance level + is_a: likelihood affected by inverse: promotes condition domain: disease or phenotypic feature range: chemical or drug or treatment @@ -3634,7 +3634,7 @@ slots: beneficial in models for: is_a: in preclinical trials for description: >- - Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, + Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity has been shown to be effective in alleviating, preventing, or delaying symptoms/ phenotypes associated with a disease, in a model system for that disease (e.g. a mouse, fly, cell line, etc). notes: >- diff --git a/src/biolink_model/scripts/classprefixes.py b/src/biolink_model/scripts/classprefixes.py index 66ae126d3..b79174fe8 100644 --- a/src/biolink_model/scripts/classprefixes.py +++ b/src/biolink_model/scripts/classprefixes.py @@ -1,5 +1,5 @@ # Auto generated from class_prefixes.yaml by pythongen.py version: 0.0.1 -# Generation date: 2024-05-10T23:04:18 +# Generation date: 2024-05-10T16:32:05 # Schema: BiolinkClassPrefixes # # id: biolink-model-class-prefixes