Merge pull request #1532 from biolink/predicate_mapping_and_inverses

Predicate inverses & tests

Makefile

@@ -141,7 +141,7 @@ test-schema: gen-project
 
 test-python:
 	cp biolink-model.yaml src/biolink_model/schema/biolink_model.yaml
-	$(RUN) python -m unittest discover -p 'test_*.py'
+	$(RUN) pytest
 
 lint:
 	cp biolink-model.yaml src/biolink_model/schema/biolink_model.yaml

biolink-model.yaml

@@ -2703,7 +2703,6 @@ slots:
       - translator_minimal
     domain: chemical entity or gene or gene product
     range: chemical entity or gene or gene product
-    inverse: response affected by
     annotations:
       canonical_predicate: true
     exact_mappings:
@@ -2719,6 +2718,7 @@ slots:
       - translator_minimal
     domain: chemical entity or gene or gene product
     range: chemical entity or gene or gene product
+    inverse: affects response to
 
   increases response to:
     description: >-
@@ -2842,7 +2842,6 @@ slots:
     range: gene
     annotations:
       canonical_predicate: true
-    inverse: has gene product
     in_subset:
       - translator_minimal
 
@@ -2883,7 +2882,6 @@ slots:
     range: gene
     annotations:
       canonical_predicate: true
-    inverse: transcribed to
     description: >-
       x is transcribed from y if and only if x is synthesized from template y
     exact_mappings:
@@ -2896,7 +2894,6 @@ slots:
     range: protein
     annotations:
       canonical_predicate: true
-    inverse: translation of
     description: >-
       x (amino acid chain/polypeptide) is the ribosomal translation of y (transcript) if and only if a ribosome
       reads y (transcript) through a series of triplet codon-amino acid adaptor activities (GO:0030533)
@@ -4525,7 +4522,6 @@ slots:
       canonical_predicate: true
     in_subset:
       - translator_minimal
-    inverse: enabled by
     exact_mappings:
       - RO:0002327
 
@@ -4572,7 +4568,6 @@ slots:
     in_subset:
       - translator_minimal
       - samples
-    inverse: derives into
     exact_mappings:
       - RO:0001000
       - FMA:derives_from
@@ -4684,7 +4679,6 @@ slots:
       opposite_of: is excipient of
     in_subset:
       - translator_minimal
-    inverse: is active ingredient of
     mappings:
       - RO:0002248
 
@@ -4838,7 +4832,6 @@ slots:
     range: occurrent
     annotations:
       canonical_predicate: true
-    inverse: preceded by
     in_subset:
       - translator_minimal
     close_mappings:

project/jsonld/biolink_model.context.jsonld

@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-10-14T23:06:39",
+      "generation_date": "2024-10-28T13:35:21",
       "source": "biolink_model.yaml"
    },
    "@context": {

project/jsonld/biolink_model.jsonld

@@ -35761,9 +35761,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "biolink_model.yaml",
-  "source_file_date": "2024-10-14T23:06:36",
-  "source_file_size": 401471,
-  "generation_date": "2024-10-14T23:06:41",
+  "source_file_date": "2024-10-28T13:35:17",
+  "source_file_size": 401272,
+  "generation_date": "2024-10-28T13:35:23",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/biolink_model.context.jsonld",