Merge pull request #1505 from biolink/issue-1480

fix for Issue #1480
biolink · Sep 23, 2024 · 67beb24 · 67beb24
2 parents 4ec7f58 + 29173ee
commit 67beb24
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diff --git a/biolink-model.yaml b/biolink-model.yaml
@@ -213,27 +213,32 @@ types:
       - Should be implemented as a stronger type
 
   iri type:
+    uri: xsd:string
     typeof: uriorcurie
     description: >-
       An IRI
 
   label type:
+    uri: xsd:string
     typeof: string
     description: >-
       A string that provides a human-readable name for an entity
 
   predicate type:
+    uri: xsd:string
     typeof: uriorcurie
     description: >-
       A CURIE from the biolink related_to hierarchy.
       For example, biolink:related_to, biolink:causes, biolink:treats.
 
   narrative text:
+    uri: xsd:string
     typeof: string
     description: >-
       A string that provides a human-readable description of something
 
   symbol type:
+    uri: xsd:string
     typeof: string
 
   frequency value:
@@ -258,9 +263,11 @@ types:
       - qud:Unit
 
   time type:
+    uri: xsd:time
     typeof: time
 
   biological sequence:
+    uri: xsd:string
     typeof: string
 
 ## ------------
@@ -3405,7 +3412,7 @@ 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.
@@ -3418,6 +3425,7 @@ slots:
       - translator_minimal
 
   condition promoted by:
+    mixin: true
     is_a: likelihood affected by
     inverse: promotes condition
     domain: disease or phenotypic feature
@@ -3593,18 +3601,24 @@ 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
@@ -3629,7 +3643,7 @@ 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: >-
@@ -3649,6 +3663,8 @@ 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
@@ -3678,6 +3694,8 @@ 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/project/graphql/biolink_model.graphql b/project/graphql/biolink_model.graphql
@@ -1,3 +1,5 @@
+# metamodel_version: 1.7.0
+# version: 4.2.2
 type AccessibleDnaRegion implements GenomicEntity, ChemicalEntityOrGeneOrGeneProduct, PhysicalEssence, OntologyClass
   {
     id: String!

diff --git a/project/jsonld/biolink_model.context.jsonld b/project/jsonld/biolink_model.context.jsonld
@@ -1,10 +1,11 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-09-23T23:41:21",
+      "generation_date": "2024-09-23T16:44:56",
       "source": "biolink_model.yaml"
    },
    "@context": {
+      "xsd": "http://www.w3.org/2001/XMLSchema#",
       "AGRKB": "https://www.alliancegenome.org/",
       "APO": {
          "@id": "http://purl.obolibrary.org/obo/APO_",
@@ -578,7 +579,6 @@
          "@id": "http://www.w3.org/2003/01/geo/wgs84_pos",
          "@prefix": true
       },
-      "xsd": "http://www.w3.org/2001/XMLSchema#",
       "@vocab": "https://w3id.org/biolink/vocab/",
       "active_in": {
          "@type": "@id",
@@ -644,12 +644,11 @@
          "@id": "affects_response_to"
       },
       "affiliation": {
-         "@type": "@id",
+         "@type": "xsd:anyURI",
          "@id": "affiliation"
       },
       "agent_type": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -733,7 +732,6 @@
       },
       "available_from": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -790,12 +788,11 @@
          "@id": "catalyzes"
       },
       "category": {
-         "@type": "@id",
+         "@type": "xsd:anyURI",
          "@id": "category"
       },
       "causal_mechanism_qualifier": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -829,7 +826,6 @@
       },
       "clinical_approval_status": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1026,7 +1022,6 @@
       },
       "drug_regulatory_status_world_wide": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1092,7 +1087,6 @@
       },
       "FDA_adverse_event_level": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1146,7 +1140,6 @@
       },
       "genome_build": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1466,7 +1459,6 @@
       },
       "highest_FDA_approval_status": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1544,7 +1536,6 @@
          "@id": "interbase_coordinate"
       },
       "iri": {
-         "@type": "@id",
          "@id": "iri"
       },
       "is_active_ingredient_of": {
@@ -1641,7 +1632,6 @@
       },
       "knowledge_level": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1700,7 +1690,6 @@
       },
       "logical_interpretation": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1720,7 +1709,6 @@
       },
       "max_research_phase": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1747,7 +1735,7 @@
          "@id": "mentions"
       },
       "mesh_terms": {
-         "@type": "@id",
+         "@type": "xsd:anyURI",
          "@id": "mesh_terms"
       },
       "missing_from": {
@@ -1828,7 +1816,6 @@
       },
       "object_direction_qualifier": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1875,7 +1862,7 @@
          "@id": "original_object"
       },
       "original_predicate": {
-         "@type": "@id",
+         "@type": "xsd:anyURI",
          "@id": "original_predicate"
       },
       "original_subject": {
@@ -1913,7 +1900,6 @@
       },
       "phase": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1953,7 +1939,6 @@
          "@id": "precedes"
       },
       "predicate": {
-         "@type": "@id",
          "@id": "rdf:predicate"
       },
       "predicate_mappings": {
@@ -2002,7 +1987,7 @@
          "@id": "publications"
       },
       "published_in": {
-         "@type": "@id",
+         "@type": "xsd:anyURI",
          "@id": "published_in"
       },
       "publisher": {
@@ -2029,7 +2014,6 @@
       },
       "reaction_direction": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -2038,7 +2022,6 @@
       },
       "reaction_side": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -2093,12 +2076,11 @@
          "@id": "resistance_associated_with"
       },
       "resource_id": {
-         "@type": "@id",
+         "@type": "xsd:anyURI",
          "@id": "resource_id"
       },
       "resource_role": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -2130,7 +2112,6 @@
       },
       "routes_of_delivery": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -2203,7 +2184,6 @@
       },
       "strand": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -2244,7 +2224,6 @@
       },
       "subject_direction_qualifier": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -2295,7 +2274,7 @@
          "@id": "supporting_document_year"
       },
       "supporting_documents": {
-         "@type": "@id",
+         "@type": "xsd:anyURI",
          "@id": "supporting_documents"
       },
       "supporting_study_cohort": {
@@ -2311,11 +2290,11 @@
          "@id": "supporting_study_metadata"
       },
       "supporting_study_method_description": {
-         "@type": "@id",
+         "@type": "xsd:anyURI",
          "@id": "supporting_study_method_description"
       },
       "supporting_study_method_type": {
-         "@type": "@id",
+         "@type": "xsd:anyURI",
          "@id": "supporting_study_method_type"
       },
       "supporting_study_size": {
@@ -2420,7 +2399,7 @@
          "@id": "update_date"
       },
       "upstream_resource_ids": {
-         "@type": "@id",
+         "@type": "xsd:anyURI",
          "@id": "upstream_resource_ids"
       },
       "url": {
@@ -2445,7 +2424,7 @@
          "@id": "xenologous_to"
       },
       "xref": {
-         "@type": "@id",
+         "@type": "xsd:anyURI",
          "@id": "xref"
       },
       "AccessibleDnaRegion": {