fix conflicts

biolink · Jul 26, 2024 · 0415dff · 0415dff
2 parents 443de05 + 1a5e4af
commit 0415dff
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Showing 15 changed files with 23,040 additions and 22,101 deletions.
diff --git a/biolink-model.yaml b/biolink-model.yaml
diff --git a/project/graphql/biolink_model.graphql b/project/graphql/biolink_model.graphql
@@ -5833,6 +5833,59 @@ type PhenotypicFeatureToEntityAssociationMixin implements FrequencyQuantifier
     hasPercentage: Double
   }
 
+type PhenotypicFeatureToPhenotypicFeatureAssociation implements PhenotypicFeatureToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin
+  {
+    id: String!
+    iri: IriType
+    name: LabelType
+    description: NarrativeText
+    hasAttribute: [Attribute]
+    deprecated: Boolean
+    subject: NamedThing!
+    predicate: PredicateType!
+    object: NamedThing!
+    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]
+    frequencyQualifier: FrequencyValue
+    subjectAspectQualifier: String
+    subjectDirectionQualifier: DirectionQualifierEnum
+    objectAspectQualifier: String
+    objectDirectionQualifier: DirectionQualifierEnum
+    qualifiedPredicate: String
+    sexQualifier: BiologicalSex
+    hasCount: Integer
+    hasTotal: Integer
+    hasQuotient: Double
+    hasPercentage: Double
+  }
+
 type PhenotypicQuality
   {
     id: String!
@@ -6678,6 +6731,7 @@ type SiRNA
 
 type SmallMolecule
   {
+    id: String!
     iri: IriType
     type: [String]
     name: LabelType
@@ -6695,7 +6749,6 @@ type SmallMolecule
     isToxic: Boolean
     hasChemicalRole: [ChemicalRole]
     isMetabolite: Boolean
-    id: String!
   }
 
 type Snv

diff --git 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": "2024-07-26T14:50:27",
+      "generation_date": "2024-07-26T14:52:24",
       "source": "biolink_model.yaml"
    },
    "@context": {
@@ -347,8 +347,8 @@
          "@prefix": true
       },
       "PFAM": "http://identifiers.org/pfam/",
-      "PHARMGKB.CHEMICAL": "https://www.pharmgkb.org/chemical/",
       "PHARMGKB.DISEASE": "https://www.pharmgkb.org/disease/",
+      "PHARMGKB.DRUG": "https://www.pharmgkb.org/chemical/",
       "PHARMGKB.GENE": "https://www.pharmgkb.org/gene/",
       "PHARMGKB.PATHWAYS": "https://www.pharmgkb.org/pathway/",
       "PHARMGKB.VARIANT": "https://www.pharmgkb.org/variant/",
@@ -3153,6 +3153,9 @@
       "PhenotypicFeatureToEntityAssociationMixin": {
          "@id": "PhenotypicFeatureToEntityAssociationMixin"
       },
+      "PhenotypicFeatureToPhenotypicFeatureAssociation": {
+         "@id": "PhenotypicFeatureToPhenotypicFeatureAssociation"
+      },
       "PhenotypicQuality": {
          "@id": "PhenotypicQuality"
       },