Merge pull request #1461 from biolink/treats_inverses

clean up spell config, extend contraindicated to include biological process, add mappings

.github/workflows/pr-codespell.yaml

@@ -19,4 +19,4 @@ jobs:
         uses: codespell-project/actions-codespell@v1
         with:
           ignore_words_list: amination,ehr,mor,nin,brite,mirgate,BRITE
-          skip: SEMMEDDB*,semmed*,.idea,.venv,.git,*.pdf,*.svg,context.*,prefix-map,biolink,docs,json-schema,graphql,biolink-model.g*,biolink-model.t*,biolink-model.s*,biolink-model.o*,biolink-model.p*
+          skip: SEMMEDDB*,semmed*,.idea,.venv,.git,*.pdf,*.svg,context.*,prefix-map,docs,json-schema,graphql,biolink-model.g*,biolink-model.t*,biolink-model.s*,biolink-model.o*,biolink-model.p*

Makefile

@@ -144,7 +144,7 @@ tests:
 	$(RUN) yamllint -c .yamllint-config infores_catalog.yaml
 	$(RUN) python scripts/verify_infores.py
 
-test: test-schema test-python test-examples lint
+test: test-schema test-python test-examples lint spell
 
 test-schema: gen-project
 
@@ -211,6 +211,9 @@ gendoc: $(DOCDIR)
 	cp $(DEST)/shacl/biolink_model.shacl.ttl $(DOCDIR)/biolink-model.shacl.ttl ; \
 	cp $(DEST)/prefixmap/* $(DOCDIR) ; \
 	cp infores_catalog.yaml $(DOCDIR) ; \
+	cp information-resource.yaml $(DOCDIR) ; \
+	cp semmed-exclude-list.yaml $(DOCDIR) ; \
+	cp semmed-exclude-list-model.yaml $(DOCDIR) ; \
 	cp predicate_mapping.yaml $(DOCDIR) ; \
 	cp biolink-model.yaml $(DOCDIR) ; \
 	cp $(SRC)/docs/*md $(DOCDIR) ; \

biolink-model.yaml

@@ -6,7 +6,7 @@ license: https://creativecommons.org/publicdomain/zero/1.0/
 
 # Version should be kept in sync with primary Git repository release tag
 
-version: 4.1.4
+version: 4.1.5
 
 
 ## ------------
@@ -3386,6 +3386,8 @@ slots:
       opposite_of: promotes condition
     in_subset:
       - translator_minimal
+    broad_mappings:
+      - SEMMEDDB:PREVENTS
 
   condition prevented by:
     inverse: preventative for condition
@@ -3427,6 +3429,8 @@ slots:
       canonical_predicate: true
     in_subset:
       - translator_minimal
+    broad_mappings:
+      - SEMMEDDB:PREDISPOSES
 
   condition predisposed by:
     is_a: likelihood affected by
@@ -3554,7 +3558,7 @@ slots:
     mixins:
       - treats or applied or studied to treat
     annotations:
-      canonical_predicate: tru
+      canonical_predicate: true
 
   in clinical trials for:
     is_a: studied to treat
@@ -5069,7 +5073,7 @@ slots:
       are pregnant as a treatment for acne), or being on a different medication (e.g. aspirin is contraindicated
       in people taking warfarin as a preventative treatment for stroke).
     domain: chemical or drug or treatment
-    range: disease or phenotypic feature
+    range: biological entity
     annotations:
       canonical_predicate: true
       opposite_of: treats
@@ -5083,7 +5087,7 @@ slots:
 
   has contraindication:
     is_a: related to at instance level
-    domain: disease or phenotypic feature
+    domain: biological entity
     range: chemical or drug or treatment
     inverse: contraindicated in
 
@@ -7248,6 +7252,7 @@ classes:
       - KEGG.GLYCAN   # G number
       - KEGG.DRUG     # D number
       - KEGG.ENVIRON  # E number
+      - KEGG
       - UMLS
     slot_usage:
       id:
@@ -8051,6 +8056,14 @@ classes:
       - STY:T019
        # Acquired Abnormality
       - STY:T020
+       # Mental or behavioral disfunction
+      - STY:T048
+      # (Cell or Molecular Dysfunction)
+      - STY:T049
+      # (Neoplastic Process)
+      - STY:T191
+      # disease susceptibility
+      - MONDO:0042489
     id_prefixes:
       - MONDO
       - DOID
@@ -8105,6 +8118,7 @@ classes:
       - FYPO:0000001  # fission yeast phenotype
       - APO:0000017  # phenotype
       - TO:0000387  # more narrowly defined here for plants; our definition conflates trait and phenotype.
+      - STY:T190
     broad_mappings:
       - BFO:0000019  # quality
       - PATO:0000001  # quality

information-resource.yaml

@@ -1,11 +1,11 @@
 ---
-id: https://w3id.org/biolink/biolink-model/infores
+id: https://w3id.org/biolink/information-resource.yaml
 name: Biolink-Model-Information-Resource
 license: https://creativecommons.org/publicdomain/zero/1.0/
 
 # Version should be kept in sync with primary Git repository release tag
 
-version: 4.1.0
+version: 4.1.5
 
 
 ## ------------

information_resource.py

@@ -1,8 +1,8 @@
 # Auto generated from information-resource.yaml by pythongen.py version: 0.0.1
-# Generation date: 2024-02-29T17:03:47
+# Generation date: 2024-03-04T09:51:24
 # Schema: Biolink-Model-Information-Resource
 #
-# id: https://w3id.org/biolink/biolink-model/infores
+# id: https://w3id.org/biolink/information-resource.yaml
 # description:
 # license: https://creativecommons.org/publicdomain/zero/1.0/
 
@@ -24,7 +24,7 @@
 from linkml_runtime.linkml_model.types import String
 
 metamodel_version = "1.7.0"
-version = "4.1.0"
+version = "4.1.5"
 
 # Overwrite dataclasses _init_fn to add **kwargs in __init__
 dataclasses._init_fn = dataclasses_init_fn_with_kwargs