Merge pull request #1491 from biolink/predicate_mappings_update

update predicate mapping to refer to qualified predicates for regulates
biolink · Sep 23, 2024 · 03914a7 · 03914a7
2 parents 7470067 + 6bddbf6
commit 03914a7
Show file tree

Hide file tree

Showing 19 changed files with 52,861 additions and 30,779 deletions.
diff --git a/biolink-model.yaml b/biolink-model.yaml
@@ -9945,6 +9945,54 @@ classes:
       anatomical context qualifier:
         range: anatomical entity
 
+  gene regulates gene association:
+    is_a: association
+    description: >-
+      Describes a regulatory relationship between two genes or gene products.
+    slots:
+      - object aspect qualifier
+      - object direction qualifier
+      - qualified predicate
+      - species context qualifier
+    slot_usage:
+      subject:
+        range: gene or gene product
+      predicate: regulates
+      object:
+        range: gene or gene product
+      object aspect qualifier:
+        range: GeneOrGeneProductOrChemicalEntityAspectEnum
+        required: true
+        description: >-
+          the aspect of the object gene or gene product that is being regulated, must be a descendant of 
+          "activity_or_abundance""
+      object direction qualifier:
+        range: DirectionQualifierEnum
+        required: true
+      qualified predicate:
+        subproperty_of: causes
+        required: true
+    examples:
+      value:
+        subject: "NCBIGene:551"
+        predicate: regulates
+        qualified_predicte: causes
+        object: "NCBIGene:1636"
+        object_aspect_qualifier: activity_or_abundance
+        object_direction_qualifier: downregulated
+
+  process regulates process association:
+    is_a: association
+    description: >-
+      Describes a regulatory relationship between two genes or gene products.
+    slot_usage:
+      subject:
+        range: biological process
+      predicate:
+        subproperty_of: regulates
+      object:
+        range: biological process
+
   chemical affects gene association:
     description: >-
       Describes an effect that a chemical has on a gene or gene product (e.g. an impact

diff --git a/predicate_mapping.yaml b/predicate_mapping.yaml
@@ -496,24 +496,32 @@ predicate mappings:
     exact matches:
       - CTD:decreases_molecular_interaction
   - mapped predicate: entity negatively regulates entity
+    object aspect qualifier: activity or abundance
     object direction qualifier: downregulated
     predicate: regulates
+    qualified predicate: causes
     exact matches:
       - RO:0002212
       - RO:0002449
   - mapped predicate: entity positively regulates entity
+    object aspect qualifier: activity or abundance
     object direction qualifier: upregulated
     predicate: regulates
+    qualified predicate: causes
     exact matches:
       - RO:0002450
   - mapped predicate: process positively regulates process
+    object aspect qualifier: activity or abundance
     object direction qualifier: upregulated
     predicate: regulates
+    qualified predicate: causes
     exact matches:
       - RO:0002213
   - mapped predicate: process negatively regulates process
+    object aspect qualifier: activity or abundance
     object direction qualifier: downregulated
     predicate: regulates
+    qualified predicate: causes
     exact matches:
       - RO:0002212
 
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!
@@ -3237,6 +3239,52 @@ interface GeneProductMixin
     xref: [Uriorcurie]
   }
 
+type GeneRegulatesGeneAssociation
+  {
+    id: String!
+    iri: IriType
+    name: LabelType
+    description: NarrativeText
+    hasAttribute: [Attribute]
+    deprecated: Boolean
+    negated: Boolean
+    qualifier: String
+    qualifiers: [OntologyClass]
+    publications: [Publication]
+    hasEvidence: [EvidenceType]
+    knowledgeSource: String
+    primaryKnowledgeSource: String
+    aggregatorKnowledgeSource: [String]
+    knowledgeLevel: KnowledgeLevelEnum!
+    agentType: AgentTypeEnum!
+    timepoint: TimeType
+    originalSubject: String
+    originalPredicate: Uriorcurie
+    originalObject: String
+    subjectCategory: OntologyClass
+    objectCategory: OntologyClass
+    subjectClosure: [String]
+    objectClosure: [String]
+    subjectCategoryClosure: [OntologyClass]
+    objectCategoryClosure: [OntologyClass]
+    subjectNamespace: String
+    objectNamespace: String
+    subjectLabelClosure: [String]
+    objectLabelClosure: [String]
+    retrievalSourceIds: [RetrievalSource]
+    pValue: Float
+    adjustedPValue: Float
+    type: [String]
+    category: [Uriorcurie]
+    objectAspectQualifier: GeneOrGeneProductOrChemicalEntityAspectEnum!
+    objectDirectionQualifier: DirectionQualifierEnum!
+    qualifiedPredicate: String!
+    speciesContextQualifier: OrganismTaxon
+    subject: GeneOrGeneProduct!
+    predicate: PredicateType!
+    object: GeneOrGeneProduct!
+  }
+
 type GeneToDiseaseAssociation implements EntityToDiseaseAssociationMixin, GeneToEntityAssociationMixin
   {
     id: String!
@@ -6166,6 +6214,48 @@ type Procedure implements ActivityAndBehavior
     category: [Uriorcurie]!
   }
 
+type ProcessRegulatesProcessAssociation
+  {
+    id: String!
+    iri: IriType
+    name: LabelType
+    description: NarrativeText
+    hasAttribute: [Attribute]
+    deprecated: Boolean
+    negated: Boolean
+    qualifier: String
+    qualifiers: [OntologyClass]
+    publications: [Publication]
+    hasEvidence: [EvidenceType]
+    knowledgeSource: String
+    primaryKnowledgeSource: String
+    aggregatorKnowledgeSource: [String]
+    knowledgeLevel: KnowledgeLevelEnum!
+    agentType: AgentTypeEnum!
+    timepoint: TimeType
+    originalSubject: String
+    originalPredicate: Uriorcurie
+    originalObject: String
+    subjectCategory: OntologyClass
+    objectCategory: OntologyClass
+    subjectClosure: [String]
+    objectClosure: [String]
+    subjectCategoryClosure: [OntologyClass]
+    objectCategoryClosure: [OntologyClass]
+    subjectNamespace: String
+    objectNamespace: String
+    subjectLabelClosure: [String]
+    objectLabelClosure: [String]
+    retrievalSourceIds: [RetrievalSource]
+    pValue: Float
+    adjustedPValue: Float
+    type: [String]
+    category: [Uriorcurie]
+    subject: BiologicalProcess!
+    predicate: PredicateType!
+    object: BiologicalProcess!
+  }
+
 type ProcessedMaterial
   {
     id: String!