Merge pull request #1296 from biolink/1279

fixes #1279 fixes #1216

biolink-model.yaml

@@ -3095,18 +3095,27 @@ slots:
    # Despite the name, note that this particular entity is
    # NOT a biolink:Association but rather, a biolink:predicate
   genetic association:
-    is_a: related to at instance level
+    deprecated: true
+    deprecated_element_has_exact_replacement: biolink:genetically_associated_with
+    is_a: associated with
+    symmetric: true
+
+  genetically associated with:
+    is_a: associated with
+    description: >-
     symmetric: true
     annotations:
       canonical_predicate: true
-    description: >-
-      Co-occurrence of a certain allele of a genetic marker and the phenotype
-      of interest in the same individuals at above-chance level
+      description: >-
+        Co-occurrence of a certain allele of a genetic marker and the phenotype
+        of interest in the same individuals at above-chance level
     exact_mappings:
       - WIKIDATA_PROPERTY:P2293
+    in_subset:
+      - translator_minimal
 
   gene associated with condition:
-    is_a: genetic association
+    is_a: genetically associated with
     description: >-
       holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence,
       contribute to, or correlate with
@@ -3126,7 +3135,7 @@ slots:
       - NCIT:R48
 
   condition associated with gene:
-    is_a: genetic association
+    is_a: genetically associated with
     aliases: ['disease associated with gene']
     description: >-
       holds between a gene and a disease or phenotypic feature that may be influenced, contribute to, or be correlated with the gene or its alleles/products
@@ -9802,48 +9811,47 @@ classes:
           - value: ClinGen:CA024716
             description: "chr13:g.32921033G>C (hg19) in ClinGen"
 
-  gene to phenotypic feature association:
+  gene to disease or phenotypic feature association:
     is_a: association
-    exact_mappings:
-      - WBVocab:Gene-Phenotype-Association
-    defining_slots:
-      - subject
-      - object
     mixins:
       - entity to phenotypic feature association mixin
       - gene to entity association mixin
+    narrow_mappings:
+      - WBVocab:Gene-Phenotype-Association
+      - dcid:DiseaseGeneAssociation
+      - SIO:000983
+    slots:
+      - subject aspect qualifier
+      - object direction qualifier
     slot_usage:
       subject:
         range: gene or gene product
         description: "gene in which variation is correlated with the phenotypic feature"
         examples:
           - value: HGNC:2197
             description: "COL1A1 (Human)"
+      subject aspect qualifier:
+        range: GeneOrGeneProductOrChemicalEntityAspectEnum
       object:
-        range: phenotypic feature
+        range: disease or phenotypic feature
+      object direction qualifier:
+        range: DirectionQualifierEnum
+      predicate:
+        subproperty_of: affects
+    comments:
+      - NCIT:R176 refers to the inverse relationship
+      - for use in describing the affect that the loss of function of a gene can have on exacerbating or ameliorating a symptom/phenotype
+      - if the relationship of the statement using this predicate is statistical in nature, please use `associated with likelihood` or one of its children.
 
   gene to disease association:
+    deprecated: true
+    deprecated_element_has_exact_replacement: biolink:gene_to_disease_or_phenotypic_feature_association
+    is_a: association
+
+  gene to phenotype association:
+    deprecated: true
+    deprecated_element_has_exact_replacement: biolink:gene_to_disease_or_phenotypic_feature_association
     is_a: association
-    comments:
-      - NCIT:R176 refers to the inverse relationship
-    exact_mappings:
-      - SIO:000983
-    close_mappings:
-      - dcid:DiseaseGeneAssociation
-    defining_slots:
-      - subject
-      - object
-    mixins:
-      - entity to disease association mixin
-      - gene to entity association mixin
-    slot_usage:
-      subject:
-        range: gene or gene product
-        description: >-
-          gene in which variation is correlated with the disease,
-          may be protective or causative or associative, or as a model
-      object:
-        range: disease
 
   druggable gene to disease association:
     is_a: gene to disease association
@@ -9881,7 +9889,7 @@ classes:
       object:
         range: gene
       predicate:
-        subproperty_of: genetic association
+        subproperty_of: genetically associated with
 
   variant to gene expression association:
     description: >-