Merge pull request #202 from monarch-initiative/add-gene-term-slot

Add gene_term slot to Genetic class for HGNC ontology binding

Author: caufieldjh

examples/gene_term_example.yaml

@@ -0,0 +1,21 @@
+# Example showing the use of gene_term slot in the Genetic class
+# This demonstrates option 2 from issue #198
+
+name: Example Disease
+category: Mendelian
+parents: []
+
+genetic:
+  - name: AGK
+    association: Causative
+    gene_term:
+      preferred_term: acylglycerol kinase
+      term:
+        id: HGNC:21869
+        label: acylglycerol kinase
+    notes: Autosomal recessive; example showing gene_term usage
+    evidence:
+      - reference: PMID:12345678
+        supports: SUPPORT
+        snippet: "Example evidence text."
+        explanation: This is an example.

src/dismech/schema/dismech.yaml

@@ -232,7 +232,10 @@ enums:
   TriggerTerm:
     description: A trigger
   GeneTerm:
-    description: A gene
+    description: A gene term from HGNC
+    comments:
+      - Uses HGNC gene nomenclature committee identifiers
+      - Validation requires exact label match with HGNC database
   CellTypeTerm:
     description: A cell type
     reachable_from:
@@ -719,6 +722,10 @@ slots:
     description: The HP term for this phenotype
     range: PhenotypeDescriptor
     inlined: true
+  gene_term:
+    description: The HGNC term for this gene
+    range: GeneDescriptor
+    inlined: true
   treatment_term:
     description: The MAXO term for this treatment/medical action
     range: TreatmentDescriptor
@@ -1258,6 +1265,10 @@ classes:
     slot_usage:
       term:
         description: Optional gene database term reference (e.g., HGNC)
+        bindings:
+          - binds_value_of: id
+            range: GeneTerm
+            obligation_level: REQUIRED
 
   CellularComponentDescriptor:
     is_a: Descriptor
@@ -1704,6 +1715,7 @@ classes:
   Genetic:
     slots:
       - name
+      - gene_term
       - presence
       - evidence
       - association