Merge pull request #1695 from biolink/g2p-confidence

add temp G2P slot to attributes.yaml, GeneToDiseaseAssociation

Author: sierra-moxon

attributes.yaml

@@ -251,3 +251,10 @@ slots:
       It is based on different inputs for curated knowledge associations vs text-mined associations vs experimental/GWAS based associations,
       but adjusts/caps scores for these types of knowledge such that they are comparable on a single scale.
     range: float
+  
+  gene2phenotype confidence category:
+    description: >-
+      A term used by EBI Gene2Phenotype to describe the confidence that the association is real.
+      GenCC confidence terms are used for different levels of confidence (enum). 
+      See https://www.ebi.ac.uk/gene2phenotype/about/terminology#g2p-confidence-section.
+    range: string

biolink-model.yaml

@@ -11576,6 +11576,7 @@ classes:
       - allelic requirement
       - qualified predicate
       - diseases confidence score
+      - gene2phenotype confidence category
     slot_usage:
       subject:
         range: gene or gene product

project/graphql/biolink_model.graphql

@@ -4027,6 +4027,7 @@ type DruggableGeneToDiseaseAssociation implements EntityToDiseaseAssociationMixi
     allelicRequirement: String
     qualifiedPredicate: Uriorcurie
     diseasesConfidenceScore: Float
+    gene2phenotypeConfidenceCategory: String
     object: Disease!
     druggableGeneCategory: DruggableGeneCategoryEnum
     subject: GeneOrGeneProduct!
@@ -4966,6 +4967,7 @@ type GeneAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMixin,
     allelicRequirement: String
     qualifiedPredicate: Uriorcurie
     diseasesConfidenceScore: Float
+    gene2phenotypeConfidenceCategory: String
     object: Disease!
     predicate: GeneToDiseasePredicateEnum!
     subject: GeneOrGeneProduct!
@@ -5116,6 +5118,7 @@ type GeneHasVariantThatContributesToDiseaseAssociation
     allelicRequirement: String
     qualifiedPredicate: Uriorcurie
     diseasesConfidenceScore: Float
+    gene2phenotypeConfidenceCategory: String
     subjectFormOrVariantQualifier: String
     subject: GeneOrGeneProduct!
     object: Disease!
@@ -5362,6 +5365,7 @@ type GeneToDiseaseAssociation implements GeneToEntityAssociationMixin
     allelicRequirement: String
     qualifiedPredicate: Uriorcurie
     diseasesConfidenceScore: Float
+    gene2phenotypeConfidenceCategory: String
     subject: GeneOrGeneProduct!
     object: Disease!
     predicate: GeneToDiseasePredicateEnum!

project/jsonld/biolink_model.context.jsonld

@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2026-01-30T16:18:42",
+      "generation_date": "2026-02-04T06:39:36",
       "source": "biolink_model.yaml"
    },
    "@context": {
@@ -1312,6 +1312,9 @@
          "@type": "@id",
          "@id": "gene_product_of"
       },
+      "gene2phenotype_confidence_category": {
+         "@id": "gene2phenotype_confidence_category"
+      },
       "gene_fusion_with": {
          "@type": "@id",
          "@id": "gene_fusion_with"

project/jsonld/biolink_model.jsonld

@@ -14846,6 +14846,19 @@
       "range": "float",
       "@type": "SlotDefinition"
     },
+    {
+      "name": "gene2phenotype_confidence_category",
+      "definition_uri": "https://w3id.org/biolink/biolink-model/attributes/gene2phenotype_confidence_category",
+      "description": "A term used by EBI Gene2Phenotype to describe the confidence that the association is real. GenCC confidence terms are used for different levels of confidence (enum).  See https://www.ebi.ac.uk/gene2phenotype/about/terminology#g2p-confidence-section.",
+      "from_schema": "https://w3id.org/biolink/biolink-model/attributes",
+      "slot_uri": "https://w3id.org/biolink/vocab/gene2phenotype_confidence_category",
+      "owner": "GeneToDiseaseAssociation",
+      "domain_of": [
+        "GeneToDiseaseAssociation"
+      ],
+      "range": "string",
+      "@type": "SlotDefinition"
+    },
     {
       "name": "attribute_name",
       "definition_uri": "https://w3id.org/biolink/vocab/name",
@@ -38167,6 +38180,7 @@
         "allelic_requirement",
         "qualified_predicate",
         "diseases_confidence_score",
+        "gene2phenotype_confidence_category",
         "gene_to_disease_association_subject",
         "gene_to_disease_association_object",
         "gene_to_disease_association_predicate"
@@ -38393,6 +38407,7 @@
         "allelic_requirement",
         "qualified_predicate",
         "diseases_confidence_score",
+        "gene2phenotype_confidence_category",
         "gene_to_disease_association_object",
         "druggable_gene_category",
         "druggable_gene_to_disease_association_subject",
@@ -39087,6 +39102,7 @@
         "allelic_requirement",
         "qualified_predicate",
         "diseases_confidence_score",
+        "gene2phenotype_confidence_category",
         "gene_to_disease_association_object",
         "gene_to_disease_association_predicate",
         "gene_as_a_model_of_disease_association_subject",
@@ -39598,6 +39614,7 @@
         "allelic_requirement",
         "qualified_predicate",
         "diseases_confidence_score",
+        "gene2phenotype_confidence_category",
         "subject_form_or_variant_qualifier",
         "gene_has_variant_that_contributes_to_disease_association_subject",
         "gene_has_variant_that_contributes_to_disease_association_object",
@@ -41484,9 +41501,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "biolink_model.yaml",
-  "source_file_date": "2026-01-30T16:18:38",
-  "source_file_size": 459779,
-  "generation_date": "2026-01-30T16:18:45",
+  "source_file_date": "2026-02-04T06:39:32",
+  "source_file_size": 459822,
+  "generation_date": "2026-02-04T06:39:38",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/biolink_model.context.jsonld",

project/jsonschema/biolink_model.schema.json

@@ -26197,6 +26197,13 @@
                         "null"
                     ]
                 },
+                "gene2phenotype_confidence_category": {
+                    "description": "A term used by EBI Gene2Phenotype to describe the confidence that the association is real. GenCC confidence terms are used for different levels of confidence (enum).  See https://www.ebi.ac.uk/gene2phenotype/about/terminology#g2p-confidence-section.",
+                    "type": [
+                        "string",
+                        "null"
+                    ]
+                },
                 "has_attribute": {
                     "description": "connects any entity to an attribute",
                     "items": {
@@ -32083,6 +32090,13 @@
                         "null"
                     ]
                 },
+                "gene2phenotype_confidence_category": {
+                    "description": "A term used by EBI Gene2Phenotype to describe the confidence that the association is real. GenCC confidence terms are used for different levels of confidence (enum).  See https://www.ebi.ac.uk/gene2phenotype/about/terminology#g2p-confidence-section.",
+                    "type": [
+                        "string",
+                        "null"
+                    ]
+                },
                 "has_attribute": {
                     "description": "connects any entity to an attribute",
                     "items": {
@@ -33125,6 +33139,13 @@
                         "null"
                     ]
                 },
+                "gene2phenotype_confidence_category": {
+                    "description": "A term used by EBI Gene2Phenotype to describe the confidence that the association is real. GenCC confidence terms are used for different levels of confidence (enum).  See https://www.ebi.ac.uk/gene2phenotype/about/terminology#g2p-confidence-section.",
+                    "type": [
+                        "string",
+                        "null"
+                    ]
+                },
                 "has_attribute": {
                     "description": "connects any entity to an attribute",
                     "items": {
@@ -34931,6 +34952,13 @@
                         "null"
                     ]
                 },
+                "gene2phenotype_confidence_category": {
+                    "description": "A term used by EBI Gene2Phenotype to describe the confidence that the association is real. GenCC confidence terms are used for different levels of confidence (enum).  See https://www.ebi.ac.uk/gene2phenotype/about/terminology#g2p-confidence-section.",
+                    "type": [
+                        "string",
+                        "null"
+                    ]
+                },
                 "has_attribute": {
                     "description": "connects any entity to an attribute",
                     "items": {