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Merge pull request #269 from alliance-genome/Split-out-genetic-modifiers
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Split out genetic modifier types
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@chris-grove
chris-grove authored Oct 23, 2024
2 parents 29e01d7 + b8c99b5 commit 7ca56f9
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Showing 2 changed files with 87 additions and 26 deletions.
84 changes: 63 additions & 21 deletions generated/jsonschema/allianceModel.schema.json
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Expand Up @@ -65,17 +65,31 @@
"$ref": "#/$defs/AffectedGenomicModel",
"description": "The AGM to which the disease ontology term is associated."
},
"disease_genetic_modifier_relation": {
"description": "A relation describing how the genetic modifier modifies the disease model. Submitted value should be a vocabulary term from the 'Disease genetic modifiers' vocabulary",
"type": "string"
"disease_genetic_modifier_agms": {
"description": "Specifies an affected genomic model (e.g. genotype) that modifies a disease model.",
"items": {
"$ref": "#/$defs/AffectedGenomicModel"
},
"type": "array"
},
"disease_genetic_modifiers": {
"description": "Specifies a genetic object that modifies the disease model. May be a gene, allele, AGM.",
"disease_genetic_modifier_alleles": {
"description": "Specifies an allele that modifies a disease model.",
"items": {
"type": "string"
"$ref": "#/$defs/Allele"
},
"type": "array"
},
"disease_genetic_modifier_genes": {
"description": "Specifies a gene that modifies a disease model.",
"items": {
"$ref": "#/$defs/Gene"
},
"type": "array"
},
"disease_genetic_modifier_relation": {
"description": "A relation describing how the genetic modifier modifies the disease model. Submitted value should be a vocabulary term from the 'Disease genetic modifiers' vocabulary",
"type": "string"
},
"disease_qualifiers": {
"description": "Submitted values should be vocabulary terms from the 'Disease qualifiers' Vocabulary",
"items": {
Expand Down Expand Up @@ -226,7 +240,7 @@
"type": "string"
},
"disease_genetic_modifier_identifiers": {
"description": "Identifiers (curie/primary_external_id/mod_internal_id) of BiologcalEntity that modifies the disease model",
"description": "Identifiers (curie/primary_external_id/mod_internal_id) of Gene, Allele or AGM that modifies the disease model",
"items": {
"type": "string"
},
Expand Down Expand Up @@ -2271,17 +2285,31 @@
"$ref": "#/$defs/Allele",
"description": "The allele to which the disease ontology term is associated."
},
"disease_genetic_modifier_relation": {
"description": "A relation describing how the genetic modifier modifies the disease model. Submitted value should be a vocabulary term from the 'Disease genetic modifiers' vocabulary",
"type": "string"
"disease_genetic_modifier_agms": {
"description": "Specifies an affected genomic model (e.g. genotype) that modifies a disease model.",
"items": {
"$ref": "#/$defs/AffectedGenomicModel"
},
"type": "array"
},
"disease_genetic_modifiers": {
"description": "Specifies a genetic object that modifies the disease model. May be a gene, allele, AGM.",
"disease_genetic_modifier_alleles": {
"description": "Specifies an allele that modifies a disease model.",
"items": {
"type": "string"
"$ref": "#/$defs/Allele"
},
"type": "array"
},
"disease_genetic_modifier_genes": {
"description": "Specifies a gene that modifies a disease model.",
"items": {
"$ref": "#/$defs/Gene"
},
"type": "array"
},
"disease_genetic_modifier_relation": {
"description": "A relation describing how the genetic modifier modifies the disease model. Submitted value should be a vocabulary term from the 'Disease genetic modifiers' vocabulary",
"type": "string"
},
"disease_qualifiers": {
"description": "Submitted values should be vocabulary terms from the 'Disease qualifiers' Vocabulary",
"items": {
Expand Down Expand Up @@ -2425,7 +2453,7 @@
"type": "string"
},
"disease_genetic_modifier_identifiers": {
"description": "Identifiers (curie/primary_external_id/mod_internal_id) of BiologcalEntity that modifies the disease model",
"description": "Identifiers (curie/primary_external_id/mod_internal_id) of Gene, Allele or AGM that modifies the disease model",
"items": {
"type": "string"
},
Expand Down Expand Up @@ -12955,17 +12983,31 @@
"$ref": "#/$defs/Gene",
"description": "The gene to which the disease ontology term is associated."
},
"disease_genetic_modifier_relation": {
"description": "A relation describing how the genetic modifier modifies the disease model. Submitted value should be a vocabulary term from the 'Disease genetic modifiers' vocabulary",
"type": "string"
"disease_genetic_modifier_agms": {
"description": "Specifies an affected genomic model (e.g. genotype) that modifies a disease model.",
"items": {
"$ref": "#/$defs/AffectedGenomicModel"
},
"type": "array"
},
"disease_genetic_modifiers": {
"description": "Specifies a genetic object that modifies the disease model. May be a gene, allele, AGM.",
"disease_genetic_modifier_alleles": {
"description": "Specifies an allele that modifies a disease model.",
"items": {
"type": "string"
"$ref": "#/$defs/Allele"
},
"type": "array"
},
"disease_genetic_modifier_genes": {
"description": "Specifies a gene that modifies a disease model.",
"items": {
"$ref": "#/$defs/Gene"
},
"type": "array"
},
"disease_genetic_modifier_relation": {
"description": "A relation describing how the genetic modifier modifies the disease model. Submitted value should be a vocabulary term from the 'Disease genetic modifiers' vocabulary",
"type": "string"
},
"disease_qualifiers": {
"description": "Submitted values should be vocabulary terms from the 'Disease qualifiers' Vocabulary",
"items": {
Expand Down Expand Up @@ -13097,7 +13139,7 @@
"type": "string"
},
"disease_genetic_modifier_identifiers": {
"description": "Identifiers (curie/primary_external_id/mod_internal_id) of BiologcalEntity that modifies the disease model",
"description": "Identifiers (curie/primary_external_id/mod_internal_id) of Gene, Allele or AGM that modifies the disease model",
"items": {
"type": "string"
},
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29 changes: 24 additions & 5 deletions model/schema/phenotypeAndDiseaseAnnotation.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -252,7 +252,9 @@ classes:
- disease_qualifiers
- genetic_sex
- secondary_data_provider
- disease_genetic_modifiers
- disease_genetic_modifier_genes
- disease_genetic_modifier_alleles
- disease_genetic_modifier_agms
- disease_genetic_modifier_relation
slot_usage:
curie:
Expand Down Expand Up @@ -735,15 +737,30 @@ slots:
The biological entity to which the disease ontology term is associated.
domain: DiseaseAnnotation
range: BiologicalEntity

disease_genetic_modifiers:

disease_genetic_modifier_genes:
description: >-
Specifies a gene that modifies a disease model.
required: false
range: Gene
multivalued: true

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

disease_genetic_modifier_agms:
description: >-
Specifies an affected genomic model (e.g. genotype) that modifies a disease model.
required: false
range: AffectedGenomicModel
multivalued: true

disease_genetic_modifier_identifiers:
description: Identifiers (curie/primary_external_id/mod_internal_id) of BiologcalEntity that modifies the disease model
description: Identifiers (curie/primary_external_id/mod_internal_id) of Gene, Allele or AGM that modifies the disease model
domain: DiseaseAnnotationDTO
range: string
multivalued: true
Expand All @@ -753,6 +770,7 @@ slots:
A relation describing how the genetic modifier modifies the disease model.
Submitted value should be a vocabulary term from the 'Disease genetic
modifiers' vocabulary
multivalued: false
range: VocabularyTerm # CV 'Disease Genetic Modifier Relation'

disease_genetic_modifier_relation_name:
Expand All @@ -761,6 +779,7 @@ slots:
modifies the disease model, selected from the 'Disease genetic modifier
relations' Vocabulary.
domain: DiseaseAnnotationDTO
multivalued: false
range: string # CV 'Disease Genetic Modifier Relation'

disease_qualifiers:
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