Skip to content

Commit

Permalink
Merge pull request #205 from alliance-genome/A-Team-updates-new-pheno…
Browse files Browse the repository at this point in the history
…types,-multiple-genetic-modifiers,-etc-

A-Team updates: new phenotypes, multiple genetic modifiers, etc.
  • Loading branch information
chris-grove authored Apr 26, 2023
2 parents 355b648 + 934a2bf commit c3f4af4
Show file tree
Hide file tree
Showing 6 changed files with 931 additions and 131 deletions.
972 changes: 858 additions & 114 deletions generated/jsonschema/allianceModel.schema.json

Large diffs are not rendered by default.

14 changes: 6 additions & 8 deletions model/schema/controlledVocabulary.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -34,13 +34,6 @@ prefixes:
schema: 'http://schema.org/'

slots:
text_synonyms:
description: >-
Free text synonym(s) of a term, used for controlled vocabulary terms; this is distinct from the
'synonyms' slot which has a range of a Synonym class object.
domain: VocabularyTerm
range: string
multivalued: true

member_terms:
description: >-
Expand Down Expand Up @@ -77,11 +70,15 @@ classes:
- name
- abbreviation
- definition
- text_synonyms
- synonyms
slot_usage:
name:
required: true
identifier: true
synonyms:
description: >-
Free text synonym(s) of a controlled vocabulary term
required: false

Vocabulary:
description: >-
Expand All @@ -96,6 +93,7 @@ classes:
required: true
identifier: true


VocabularyTermSet:
is_a: AuditedObject
description: >-
Expand Down
10 changes: 8 additions & 2 deletions model/schema/core.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -804,8 +804,9 @@ slots:

synonyms:
description: >-
Placeholder? Some objects still use this slot. Not clear how it fits in
with NameSlotAnnotation (which captures evidence).
A generic free-text field for objects that only have string representation of one
or more synonyms and do not require meta data or attribution; if meta data or attribution
are required to be captured for individual synonyms, consider the NameSlotAnnotation class
range: string
required: false
multivalued: true
Expand Down Expand Up @@ -857,6 +858,11 @@ slots:
The model organism database (MOD) identifier/curie for the object
range: string

mod_internal_id:
description: >-
The model organism database (MOD) internal identifier for the object
range: string

first_name:
description: first name of a person
range: string
Expand Down
43 changes: 42 additions & 1 deletion model/schema/ontologyTerm.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -216,7 +216,6 @@ classes:
is_a: OntologyTerm
abstract: true


FBDVTerm:
is_a: StageTerm

Expand Down Expand Up @@ -286,9 +285,51 @@ classes:
XPOTerm:
is_a: PhenotypeTerm
description: >-
A phenotype ontology term from the Xenopus Phenotype Ontology (XPO).
PURL: http://purl.obolibrary.org/obo/xpo.owl
MPTerm:
is_a: PhenotypeTerm
description: >-
A phenotype ontology term from the Mammalian Phenotype (MP) Ontology.
PURL: http://purl.obolibrary.org/obo/mp.owl
HPTerm:
is_a: PhenotypeTerm
description: >-
A phenotype ontology term from the Human Phenotype (HP) Ontology.
PURL: http://purl.obolibrary.org/obo/hp.owl
WBPhenotypeTerm:
is_a: PhenotypeTerm
description: >-
A phenotype ontology term from the (WormBase) C. elegans Phenotype Ontology (WBPhenotype).
PURL: http://purl.obolibrary.org/obo/wbphenotype.owl
APOTerm:
is_a: PhenotypeTerm
description: >-
A phenotype ontology term from the Ascomycete Phenotype Ontology (APO).
PURL: http://purl.obolibrary.org/obo/APO.owl
DPOTerm:
is_a: PhenotypeTerm
description: >-
A phenotype ontology term from the Drosophila Phenotype Ontology (DPO).
PURL: http://purl.obolibrary.org/obo/dpo.owl
PATOTerm:
is_a: OntologyTerm
description: >-
An ontology term from the Phenotype and Trait Ontology (PATO).
PURL: http://purl.obolibrary.org/obo/PATO.owl
OBITerm:
is_a: OntologyTerm
description: >-
An ontology term from the Ontology for Biomedical Investigations (OBI).
PURL: http://purl.obolibrary.org/obo/obi.owl
ATPTerm:
is_a: OntologyTerm
Expand Down
18 changes: 14 additions & 4 deletions model/schema/phenotypeAndDiseaseAnnotation.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -183,6 +183,7 @@ classes:
- curie
- unique_id
- mod_entity_id
- mod_internal_id
- negated
- evidence_codes
- single_reference
Expand All @@ -194,7 +195,7 @@ classes:
- related_notes
- data_provider
- secondary_data_provider
- disease_genetic_modifier
- disease_genetic_modifiers
- disease_genetic_modifier_relation
slot_usage:
curie:
Expand All @@ -211,6 +212,12 @@ classes:
description: >-
The model organism database (MOD) identifier/curie for the disease annotation. Currently only
used by WormBase for disease annotations, e.g. "WBDOannot00000907"
required: false
mod_internal_id:
description: >-
The model organism database (MOD) internal identifier for the disease annotation. When available,
this is used for determination of distinctness instead of the Unique ID field.
required: false
subject:
required: true
description: >-
Expand Down Expand Up @@ -268,6 +275,7 @@ classes:
- disease_relation_name
- do_term_curie
- mod_entity_id
- mod_internal_id
- negated
- evidence_curies
- evidence_code_curies
Expand All @@ -280,7 +288,7 @@ classes:
- note_dtos
- data_provider_dto
- secondary_data_provider_dto
- disease_genetic_modifier_curie
- disease_genetic_modifier_curies
- disease_genetic_modifier_relation_name

GeneDiseaseAnnotation:
Expand Down Expand Up @@ -681,15 +689,17 @@ slots:
inlined: true
inlined_as_list: true

disease_genetic_modifier:
disease_genetic_modifiers:
description: >-
Specifies a genetic object that modifies the disease model. May be a gene, allele, AGM.
required: false
multivalued: true

disease_genetic_modifier_curie:
disease_genetic_modifier_curies:
description: Curie of BiologcalEntity that modifies the disease model
domain: DiseaseAnnotationDTO
range: string
multivalued: true

disease_genetic_modifier_relation:
description: >-
Expand Down
5 changes: 3 additions & 2 deletions test/data/wb_disease_test.json
Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@
],
"genetic_sex_name": "hermaphrodite",
"mod_entity_id": "WBDOannot00001032",
"mod_internal_id": "MGI:diseaseannotation_239930183_295748146",
"updated_by_curie": "WB:WBPerson324",
"internal": false,
"negated": false,
Expand Down Expand Up @@ -90,7 +91,7 @@
"internal": false
}
],
"disease_genetic_modifier_curie": "WB:WBStrain00035193",
"disease_genetic_modifier_curies": ["WB:WBStrain00035193"],
"disease_genetic_modifier_relation_name": "ameliorated_by",
"evidence_code_curies": [
"ECO:0000315",
Expand Down Expand Up @@ -122,7 +123,7 @@
"internal": false
},
"date_updated": "2019-03-08T00:00:00+00:00",
"disease_genetic_modifier_curie": "WB:WBVar00250993",
"disease_genetic_modifier_curies": ["WB:WBVar00250993"],
"disease_genetic_modifier_relation_name": "exacerbated_by",
"evidence_code_curies": [
"ECO:0000315",
Expand Down

0 comments on commit c3f4af4

Please sign in to comment.