fix for Issue #1480

biolink-model.yaml

@@ -3403,7 +3403,7 @@ slots:
 
   promotes condition:
     mixin: true
-    is_a: related to at instance level
+    is_a: affects likelihood of
     description: >-
       Holds between a substance, procedure, or activity and a medical condition (disease or phenotypic feature),
       and states that the  substance, procedure, or activity is able to promote it manifesting in the first place.
@@ -3416,6 +3416,7 @@ slots:
       - translator_minimal
 
   condition promoted by:
+    mixin: true
     is_a: likelihood affected by
     inverse: promotes condition
     domain: disease or phenotypic feature
@@ -3591,18 +3592,24 @@ slots:
 
   tested by clinical trials of:
     is_a: treated in studies by
+    mixins:
+      - subject of treatment application or study for treatment 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
+    mixins:
+      - subject of treatment application or study for treatment 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
+    mixins:
+      - subject of treatment application or study for treatment by
     inverse: in preclinical trials for
     domain: disease or phenotypic feature
     range: chemical or drug or treatment
@@ -3627,7 +3634,7 @@ slots:
   beneficial in models for:
     is_a: in preclinical trials for
     description: >-
-      Holds between an  substance, procedure, or activity and a medical condition, and reports that the  substance,
+      Holds between an  substance, procedure, or activity and a medical condition, and reports that the substance,
       procedure, or activity has been shown to be effective in alleviating, preventing, or delaying symptoms/
       phenotypes associated with a disease, in a model system for that disease (e.g. a mouse, fly, cell line, etc).
     notes: >-
@@ -3647,6 +3654,8 @@ slots:
 
   models demonstrating benefits for:
     is_a: tested by preclinical trials of
+    mixins:
+      - subject of treatment application or study for treatment by
     inverse: beneficial in models for
     domain: disease or phenotypic feature
     range: chemical or drug or treatment
@@ -3676,6 +3685,8 @@ slots:
 
   treatment applications from:
     is_a: related to at instance level
+    mixins:
+      - subject of treatment application or study for treatment by
     inverse: applied to treat
     domain: disease or phenotypic feature
     range: chemical or drug or treatment

project/jsonld/biolink_model.context.jsonld

@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-05-10T23:03:10",
+      "generation_date": "2024-05-10T16:31:05",
       "source": "biolink_model.yaml"
    },
    "@context": {

project/jsonld/biolink_model.jsonld

@@ -7688,7 +7688,7 @@
         "translator_minimal"
       ],
       "from_schema": "https://w3id.org/biolink/biolink-model",
-      "is_a": "related_to_at_instance_level",
+      "is_a": "affects_likelihood_of",
       "mixin": true,
       "domain": "ChemicalOrDrugOrTreatment",
       "slot_uri": "https://w3id.org/biolink/vocab/promotes_condition",
@@ -7704,6 +7704,7 @@
       "definition_uri": "https://w3id.org/biolink/vocab/condition_promoted_by",
       "from_schema": "https://w3id.org/biolink/biolink-model",
       "is_a": "likelihood_affected_by",
+      "mixin": true,
       "domain": "DiseaseOrPhenotypicFeature",
       "slot_uri": "https://w3id.org/biolink/vocab/condition_promoted_by",
       "multivalued": true,
@@ -7979,6 +7980,9 @@
       "definition_uri": "https://w3id.org/biolink/vocab/tested_by_clinical_trials_of",
       "from_schema": "https://w3id.org/biolink/biolink-model",
       "is_a": "treated_in_studies_by",
+      "mixins": [
+        "subject_of_treatment_application_or_study_for_treatment_by"
+      ],
       "domain": "DiseaseOrPhenotypicFeature",
       "slot_uri": "https://w3id.org/biolink/vocab/tested_by_clinical_trials_of",
       "multivalued": true,
@@ -7994,6 +7998,9 @@
       "definition_uri": "https://w3id.org/biolink/vocab/treated_in_studies_by",
       "from_schema": "https://w3id.org/biolink/biolink-model",
       "is_a": "treated_by",
+      "mixins": [
+        "subject_of_treatment_application_or_study_for_treatment_by"
+      ],
       "domain": "DiseaseOrPhenotypicFeature",
       "slot_uri": "https://w3id.org/biolink/vocab/treated_in_studies_by",
       "multivalued": true,
@@ -8009,6 +8016,9 @@
       "definition_uri": "https://w3id.org/biolink/vocab/tested_by_preclinical_trials_of",
       "from_schema": "https://w3id.org/biolink/biolink-model",
       "is_a": "treated_in_studies_by",
+      "mixins": [
+        "subject_of_treatment_application_or_study_for_treatment_by"
+      ],
       "domain": "DiseaseOrPhenotypicFeature",
       "slot_uri": "https://w3id.org/biolink/vocab/tested_by_preclinical_trials_of",
       "multivalued": true,
@@ -8057,7 +8067,7 @@
           "@type": "Annotation"
         }
       ],
-      "description": "Holds between an  substance, procedure, or activity and a medical condition, and reports that the  substance, procedure, or activity has been shown to be effective in alleviating, preventing, or delaying symptoms/ phenotypes associated with a disease, in a model system for that disease (e.g. a mouse, fly, cell line, etc).",
+      "description": "Holds between an  substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity has been shown to be effective in alleviating, preventing, or delaying symptoms/ phenotypes associated with a disease, in a model system for that disease (e.g. a mouse, fly, cell line, etc).",
       "notes": [
         "This predicate would be used to represent Model Organism Database (MOD) records reporting that an intervention alleviated phenotypes associated with a human disease in a model organism designated as a model of that disease. (e.g. a ZFIN record reporting that treatment with Braf Inhibitors reduced the abnormal brain cell proliferation phenotype of zebrafish used to model the human disease Kabuki Syndrome) ."
       ],
@@ -8083,6 +8093,9 @@
       "definition_uri": "https://w3id.org/biolink/vocab/models_demonstrating_benefits_for",
       "from_schema": "https://w3id.org/biolink/biolink-model",
       "is_a": "tested_by_preclinical_trials_of",
+      "mixins": [
+        "subject_of_treatment_application_or_study_for_treatment_by"
+      ],
       "domain": "DiseaseOrPhenotypicFeature",
       "slot_uri": "https://w3id.org/biolink/vocab/models_demonstrating_benefits_for",
       "multivalued": true,
@@ -8134,6 +8147,9 @@
       "definition_uri": "https://w3id.org/biolink/vocab/treatment_applications_from",
       "from_schema": "https://w3id.org/biolink/biolink-model",
       "is_a": "related_to_at_instance_level",
+      "mixins": [
+        "subject_of_treatment_application_or_study_for_treatment_by"
+      ],
       "domain": "DiseaseOrPhenotypicFeature",
       "slot_uri": "https://w3id.org/biolink/vocab/treatment_applications_from",
       "multivalued": true,
@@ -35037,9 +35053,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "biolink_model.yaml",
-  "source_file_date": "2024-05-10T23:03:07",
-  "source_file_size": 393015,
-  "generation_date": "2024-05-10T23:03:12",
+  "source_file_date": "2024-05-10T16:31:01",
+  "source_file_size": 393418,
+  "generation_date": "2024-05-10T16:31:06",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/biolink_model.context.jsonld",