fix spacing

biolink · Oct 14, 2024 · 99d28ac · 99d28ac
1 parent ed86974
commit 99d28ac
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Showing 13 changed files with 24,834 additions and 24,459 deletions.
diff --git a/project/graphql/biolink_model.graphql b/project/graphql/biolink_model.graphql
@@ -403,6 +403,7 @@ type BehaviorToBehavioralFeatureAssociation implements EntityToPhenotypicFeature
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -678,6 +679,7 @@ type CaseToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureAsso
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -730,6 +732,7 @@ type CausalGeneToDiseaseAssociation implements EntityToDiseaseAssociationMixin,
     objectAspectQualifier: String
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -1869,6 +1872,7 @@ type CorrelatedGeneToDiseaseAssociation implements EntityToDiseaseAssociationMix
     objectAspectQualifier: String
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -2251,6 +2255,7 @@ type DiseaseToPhenotypicFeatureAssociation implements FrequencyQuantifier, Entit
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
   }
 
 type Drug implements ChemicalOrDrugOrTreatment, OntologyClass
@@ -2439,6 +2444,7 @@ type DruggableGeneToDiseaseAssociation implements EntityToDiseaseAssociationMixi
     objectAspectQualifier: String
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -2610,6 +2616,7 @@ type EntityToPhenotypicFeatureAssociationMixin implements FrequencyQuantifier
     predicate: PredicateType!
     object: PhenotypicFeature!
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -2894,6 +2901,7 @@ type ExposureEventToPhenotypicFeatureAssociation implements EntityToPhenotypicFe
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -3161,6 +3169,7 @@ type GeneAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMixin,
     objectAspectQualifier: String
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -3246,6 +3255,7 @@ type GeneHasVariantThatContributesToDiseaseAssociation
     objectAspectQualifier: String
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -3368,6 +3378,7 @@ type GeneToDiseaseAssociation implements EntityToDiseaseAssociationMixin, GeneTo
     objectAspectQualifier: String
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -3424,6 +3435,7 @@ type GeneToDiseaseOrPhenotypicFeatureAssociation implements EntityToPhenotypicFe
     objectAspectQualifier: String
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -3833,6 +3845,7 @@ type GeneToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureAsso
     objectAspectQualifier: String
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -4214,6 +4227,7 @@ type GenotypeToPhenotypicFeatureAssociation implements EntityToPhenotypicFeature
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double
@@ -6007,6 +6021,7 @@ type PhenotypicFeatureToPhenotypicFeatureAssociation implements PhenotypicFeatur
     hasTotal: Integer
     hasQuotient: Double
     hasPercentage: Double
+    diseaseContextQualifier: Disease
   }
 
 type PhenotypicQuality
@@ -7485,6 +7500,7 @@ type VariantToPhenotypicFeatureAssociation implements VariantToEntityAssociation
     objectDirectionQualifier: DirectionQualifierEnum
     qualifiedPredicate: String
     sexQualifier: BiologicalSex
+    diseaseContextQualifier: Disease
     hasCount: Integer
     hasTotal: Integer
     hasQuotient: Double

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": "2024-10-10T23:59:51",
+      "generation_date": "2024-10-14T15:38:39",
       "source": "biolink_model.yaml"
    },
    "@context": {
@@ -998,6 +998,10 @@
          "@type": "@id",
          "@id": "directly_physically_interacts_with"
       },
+      "disease_context_qualifier": {
+         "@type": "@id",
+         "@id": "disease_context_qualifier"
+      },
       "disease_has_basis_in": {
          "@type": "@id",
          "@id": "disease_has_basis_in"

diff --git a/project/jsonld/biolink_model.jsonld b/project/jsonld/biolink_model.jsonld
@@ -4574,6 +4574,34 @@
       "range": "OrganismTaxon",
       "@type": "SlotDefinition"
     },
+    {
+      "name": "disease_context_qualifier",
+      "definition_uri": "https://w3id.org/biolink/vocab/disease_context_qualifier",
+      "description": "A context qualifier representing a disease or condition in which a relationship expressed in an association took place.",
+      "examples": [
+        {
+          "value": "MONDO:0004979",
+          "@type": "Example"
+        },
+        {
+          "value": "MONDO:0005148",
+          "@type": "Example"
+        }
+      ],
+      "in_subset": [
+        "translator_minimal"
+      ],
+      "from_schema": "https://w3id.org/biolink/biolink-model",
+      "is_a": "context_qualifier",
+      "domain": "Association",
+      "slot_uri": "https://w3id.org/biolink/vocab/disease_context_qualifier",
+      "owner": "EntityToPhenotypicFeatureAssociationMixin",
+      "domain_of": [
+        "EntityToPhenotypicFeatureAssociationMixin"
+      ],
+      "range": "Disease",
+      "@type": "SlotDefinition"
+    },
     {
       "name": "qualifiers",
       "definition_uri": "https://w3id.org/biolink/vocab/qualifiers",
@@ -32077,6 +32105,7 @@
         "predicate",
         "entity_to_phenotypic_feature_association_mixin_object",
         "sex_qualifier",
+        "disease_context_qualifier",
         "has_count",
         "has_total",
         "has_quotient",
@@ -32181,7 +32210,8 @@
         "has_count",
         "has_total",
         "has_quotient",
-        "has_percentage"
+        "has_percentage",
+        "disease_context_qualifier"
       ],
       "slot_usage": {},
       "class_uri": "https://w3id.org/biolink/vocab/PhenotypicFeatureToPhenotypicFeatureAssociation",
@@ -32491,6 +32521,7 @@
         "object_direction_qualifier",
         "qualified_predicate",
         "sex_qualifier",
+        "disease_context_qualifier",
         "has_count",
         "has_total",
         "has_quotient",
@@ -32560,6 +32591,7 @@
         "object_direction_qualifier",
         "qualified_predicate",
         "sex_qualifier",
+        "disease_context_qualifier",
         "has_count",
         "has_total",
         "has_quotient",
@@ -32638,7 +32670,8 @@
         "object_aspect_qualifier",
         "object_direction_qualifier",
         "qualified_predicate",
-        "sex_qualifier"
+        "sex_qualifier",
+        "disease_context_qualifier"
       ],
       "slot_usage": {},
       "class_uri": "https://w3id.org/biolink/vocab/DiseaseToPhenotypicFeatureAssociation",
@@ -32705,6 +32738,7 @@
         "object_direction_qualifier",
         "qualified_predicate",
         "sex_qualifier",
+        "disease_context_qualifier",
         "has_count",
         "has_total",
         "has_quotient",
@@ -32774,6 +32808,7 @@
         "object_direction_qualifier",
         "qualified_predicate",
         "sex_qualifier",
+        "disease_context_qualifier",
         "has_count",
         "has_total",
         "has_quotient",
@@ -32894,6 +32929,7 @@
         "object_aspect_qualifier",
         "qualified_predicate",
         "sex_qualifier",
+        "disease_context_qualifier",
         "has_count",
         "has_total",
         "has_quotient",
@@ -32960,6 +32996,7 @@
         "object_aspect_qualifier",
         "qualified_predicate",
         "sex_qualifier",
+        "disease_context_qualifier",
         "has_count",
         "has_total",
         "has_quotient",
@@ -33038,6 +33075,7 @@
         "object_aspect_qualifier",
         "qualified_predicate",
         "sex_qualifier",
+        "disease_context_qualifier",
         "has_count",
         "has_total",
         "has_quotient",
@@ -33107,6 +33145,7 @@
         "object_aspect_qualifier",
         "qualified_predicate",
         "sex_qualifier",
+        "disease_context_qualifier",
         "has_count",
         "has_total",
         "has_quotient",
@@ -33176,6 +33215,7 @@
         "object_aspect_qualifier",
         "qualified_predicate",
         "sex_qualifier",
+        "disease_context_qualifier",
         "has_count",
         "has_total",
         "has_quotient",
@@ -33243,6 +33283,7 @@
         "object_aspect_qualifier",
         "qualified_predicate",
         "sex_qualifier",
+        "disease_context_qualifier",
         "has_count",
         "has_total",
         "has_quotient",
@@ -33629,6 +33670,7 @@
         "object_direction_qualifier",
         "qualified_predicate",
         "sex_qualifier",
+        "disease_context_qualifier",
         "has_count",
         "has_total",
         "has_quotient",
@@ -33845,6 +33887,7 @@
         "object_aspect_qualifier",
         "qualified_predicate",
         "sex_qualifier",
+        "disease_context_qualifier",
         "has_count",
         "has_total",
         "has_quotient",
@@ -34280,6 +34323,7 @@
         "object_aspect_qualifier",
         "qualified_predicate",
         "sex_qualifier",
+        "disease_context_qualifier",
         "has_count",
         "has_total",
         "has_quotient",
@@ -35717,9 +35761,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "biolink_model.yaml",
-  "source_file_date": "2024-10-10T23:59:47",
-  "source_file_size": 401060,
-  "generation_date": "2024-10-10T23:59:53",
+  "source_file_date": "2024-10-14T15:38:34",
+  "source_file_size": 401471,
+  "generation_date": "2024-10-14T15:38:41",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/biolink_model.context.jsonld",