Merge pull request #1460 from biolink/treats_inverses

adding inverses for treats hierarchy not currently inversed

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: 4.1.0
+version: 4.1.4
 
 
 ## ------------
@@ -3407,6 +3407,12 @@ slots:
     in_subset:
       - translator_minimal
 
+  condition promoted by:
+    is_a: likelihood affected by
+    inverse: promotes condition
+    domain: disease or phenotypic feature
+    range: chemical or drug or treatment
+
   predisposes to condition:
     aliases: ['risk factor for']
     is_a: affects likelihood of
@@ -3423,12 +3429,10 @@ slots:
       - translator_minimal
 
   condition predisposed by:
+    is_a: likelihood affected by
     inverse: predisposes to condition
-    is_a: related to at instance level
     domain: disease or phenotypic feature
     range: chemical or drug or treatment
-    in_subset:
-      - translator_minimal
 
   exacerbates condition:
     aliases: ['exacerbates', 'detrimental for condition']
@@ -3550,13 +3554,7 @@ slots:
     mixins:
       - treats or applied or studied to treat
     annotations:
-      canonical_predicate: true
-
-  studied for treatment with:
-    domain: disease or phenotypic feature
-    range: chemical or drug or treatment
-    # range: chemical or drug or treatment
-    inverse: studied to treat
+      canonical_predicate: tru
 
   in clinical trials for:
     is_a: studied to treat
@@ -3579,6 +3577,24 @@ slots:
       - translator_minimal
   # TODO: add inverse
 
+  tested by clinical trials of:
+    is_a: treated in studies by
+    inverse: in clinical trials for
+    domain: disease or phenotypic feature
+    range: chemical or drug or treatment
+
+  treated in studies by:
+    is_a: treated by
+    inverse: studied to treat
+    domain: disease or phenotypic feature
+    range: chemical or drug or treatment
+
+  tested by preclinical trials of:
+    is_a: treated in studies by
+    inverse: in preclinical trials for
+    domain: disease or phenotypic feature
+    range: chemical or drug or treatment
+
   in preclinical trials for:
     is_a: studied to treat
     description: >-
@@ -3617,6 +3633,12 @@ slots:
       - translator_minimal
     # TODO: need inverse of beneficial_in_models_for
 
+  models demonstrating benefits for:
+    is_a: tested by preclinical trials of
+    inverse: beneficial in models for
+    domain: disease or phenotypic feature
+    range: chemical or drug or treatment
+
   applied to treat:
     aliases: ['administered to treat', 'used to treat', 'given to treat']
     is_a: related to at instance level
@@ -3640,6 +3662,12 @@ slots:
       - translator_minimal
    # TODO: need an inverse for taken to treat
 
+  treatment applications from:
+    is_a: related to at instance level
+    inverse: applied to treat
+    domain: disease or phenotypic feature
+    range: chemical or drug or treatment
+
   treats or applied or studied to treat:
     mixin: true
     description: >-
@@ -3660,6 +3688,12 @@ slots:
     exact_mappings:
       - SEMMEDDB:TREATS
 
+  subject of treatment, application, or study for treatment by:
+    mixin: true
+    domain: disease or phenotypic feature
+    range: chemical or drug or treatment
+    inverse: treats or applied or studied to treat
+
   correlated with:
     is_a: associated with
     description: >-

information_resource.py

@@ -1,5 +1,5 @@
 # Auto generated from information-resource.yaml by pythongen.py version: 0.0.1
-# Generation date: 2023-12-15T10:29:39
+# Generation date: 2024-02-29T17:03:47
 # Schema: Biolink-Model-Information-Resource
 #
 # id: https://w3id.org/biolink/biolink-model/infores
@@ -24,7 +24,7 @@
 from linkml_runtime.linkml_model.types import String
 
 metamodel_version = "1.7.0"
-version = "4.0.0"
+version = "4.1.0"
 
 # Overwrite dataclasses _init_fn to add **kwargs in __init__
 dataclasses._init_fn = dataclasses_init_fn_with_kwargs

project/jsonld/biolink_model.context.jsonld

@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-03-01T00:50:06",
+      "generation_date": "2024-02-29T17:01:10",
       "source": "biolink_model.yaml"
    },
    "@context": {
@@ -785,6 +785,9 @@
       "condition_prevented_by": {
          "@type": "@id"
       },
+      "condition_promoted_by": {
+         "@type": "@id"
+      },
       "consumed_by": {
          "@type": "@id"
       },
@@ -1370,6 +1373,9 @@
       "models": {
          "@type": "@id"
       },
+      "models_demonstrating_benefits_for": {
+         "@type": "@id"
+      },
       "name": {
          "@id": "rdfs:label"
       },
@@ -1650,9 +1656,6 @@
             "meaning": "@id"
          }
       },
-      "studied_for_treatment_with": {
-         "@type": "@id"
-      },
       "studied_to_treat": {
          "@type": "@id"
       },
@@ -1680,6 +1683,9 @@
       "subject_location_in_text": {
          "@type": "xsd:integer"
       },
+      "subject_of_treatment_application_or_study_for_treatment_by": {
+         "@type": "@id"
+      },
       "superclass_of": {
          "@type": "@id"
       },
@@ -1716,6 +1722,12 @@
       "temporally_related_to": {
          "@type": "@id"
       },
+      "tested_by_clinical_trials_of": {
+         "@type": "@id"
+      },
+      "tested_by_preclinical_trials_of": {
+         "@type": "@id"
+      },
       "timepoint": {
          "@type": "xsd:time"
       },
@@ -1740,9 +1752,18 @@
       "treated_by": {
          "@type": "@id"
       },
+      "treated_in_studies_by": {
+         "@type": "@id"
+      },
+      "treatment_applications_from": {
+         "@type": "@id"
+      },
       "treats": {
          "@type": "@id"
       },
+      "treats_or_applied_or_studied_to_treat": {
+         "@type": "@id"
+      },
       "type": {
          "@id": "rdf:type"
       },