add subject and object specialization qualfiiers to handle MAXO and p…

…ossibly GO-CAM representations in Biolink

biolink-model.yaml

@@ -1316,6 +1316,26 @@ slots:
     in_subset:
       - translator_minimal
 
+  specialization qualifier:
+    is_a: qualifier
+    abstract: true
+    description: >-
+      A qualifier that composes with a core subject/object concept to define a more specific version of the 
+      subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept 
+      and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the
+      subject identifier.
+    examples:
+        - value: CHEBI:5118  # fluoxetine
+          description: >-
+            In a MAXO annotation this would be a specialization in treatment of a disease. For example, 
+            fluoxetine would be a specialization of the MAXO term 'serotonin-norepinephrine reuptake inhibitor agent 
+            therapy' as a treatment for the HP term 'Fatigable muscle weakness' in the context of the MONDO term
+            'congenital myasthenic syndrome '4A.'
+        - value: GO:0005634  # nucleus
+          description: >-
+            In an expression annotation this would be a specialization in location of an anatomical entity. For example,
+            "expression in the nucleus of hepatic cells" would be a specialization of "expression in hepatic cells"
+
   aspect qualifier:
     is_a: qualifier
     abstract: true
@@ -1440,6 +1460,17 @@ slots:
     in_subset:
       - translator_minimal
 
+  subject specialization qualifier:
+    is_a: specialization qualifier
+    description: >-
+      A qualifier that composes with a core subject/object concept to define a more specific version of the 
+      subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept 
+      and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the
+      subject identifier.
+    in_subset:
+      - translator_minimal
+    range: uriorcurie
+
   subject form or variant qualifier:
     description: >-
       A qualifier that composes with a core subject/object concept to define a specific type, variant,
@@ -1506,6 +1537,17 @@ slots:
     in_subset:
       - translator_minimal
 
+  object specialization qualifier:
+    is_a: specialization qualifier
+    description: >-
+      A qualifier that composes with a core subject/object concept to define a more specific version of the 
+      subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept 
+      and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the
+      subject identifier.
+    in_subset:
+      - translator_minimal
+    range: uriorcurie
+
   object form or variant qualifier:
     description: >-
       A qualifier that composes with a core subject/object concept to define a specific type, variant,
@@ -9821,7 +9863,7 @@ classes:
   chemical or drug or treatment to disease or phenotypic feature association:
     description: >-
       This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature
-      where the disesae or phenotypic feature is a secondary undesirable effect.
+      where the disease or phenotypic feature is a secondary undesirable effect.
     is_a: association
     defining_slots:
       - subject
@@ -10337,6 +10379,9 @@ classes:
       - object
       - sex qualifier
       - disease context qualifier
+      - subject specialization qualifier
+      - object specialization qualifier
+      - anatomical context qualifier
     defining_slots:
       - object
     slot_usage:

project/jsonld/biolink_model.context.jsonld

@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-10-28T20:58:55",
+      "generation_date": "2024-11-07T15:54:30",
       "source": "biolink_model.yaml"
    },
    "@context": {
@@ -2166,6 +2166,9 @@
       "source_web_page": {
          "@id": "source_web_page"
       },
+      "specialization_qualifier": {
+         "@id": "specialization_qualifier"
+      },
       "species_context_qualifier": {
          "@type": "@id",
          "@id": "species_context_qualifier"
@@ -2257,6 +2260,9 @@
       "subject_part_qualifier": {
          "@id": "subject_part_qualifier"
       },
+      "subject_specialization_qualifier": {
+         "@id": "subject_specialization_qualifier"
+      },
       "summary": {
          "@id": "summary"
       },

project/jsonld/biolink_model.jsonld

@@ -3905,6 +3905,31 @@
       "range": "string",
       "@type": "SlotDefinition"
     },
+    {
+      "name": "specialization_qualifier",
+      "definition_uri": "https://w3id.org/biolink/vocab/specialization_qualifier",
+      "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the  subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept  and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.",
+      "examples": [
+        {
+          "value": "CHEBI:24431",
+          "description": "In a MAXO annotation this would be a specialization in treatment of a disease. For example,  fluoxetine would be a specialization of the MAXO term 'serotonin-norepinephrine reuptake inhibitor agent  therapy' as a treatment for the HP term 'Fatigable muscle weakness' in the context of the MONDO term 'congenital myasthenic syndrome '4A.'",
+          "@type": "Example"
+        },
+        {
+          "value": "CL:0000123",
+          "description": "In an expression annotation this would be a specialization in location of an anatomical entity. For example, \"expression in the nucleas of hepatic cells\" would be a specialization of \"expression in hepatic cells\"",
+          "@type": "Example"
+        }
+      ],
+      "from_schema": "https://w3id.org/biolink/biolink-model",
+      "is_a": "qualifier",
+      "abstract": true,
+      "domain": "Association",
+      "slot_uri": "https://w3id.org/biolink/vocab/specialization_qualifier",
+      "owner": "specialization_qualifier",
+      "range": "string",
+      "@type": "SlotDefinition"
+    },
     {
       "name": "aspect_qualifier",
       "definition_uri": "https://w3id.org/biolink/vocab/aspect_qualifier",
@@ -4136,6 +4161,15 @@
       "range": "string",
       "@type": "SlotDefinition"
     },
+    {
+      "name": "subject_specialization_qualifier",
+      "definition_uri": "https://w3id.org/biolink/vocab/subject_specialization_qualifier",
+      "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the  subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept  and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.",
+      "from_schema": "https://w3id.org/biolink/biolink-model",
+      "slot_uri": "https://w3id.org/biolink/vocab/subject_specialization_qualifier",
+      "range": "string",
+      "@type": "SlotDefinition"
+    },
     {
       "name": "subject_form_or_variant_qualifier",
       "definition_uri": "https://w3id.org/biolink/vocab/subject_form_or_variant_qualifier",
@@ -35761,9 +35795,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "biolink_model.yaml",
-  "source_file_date": "2024-10-28T20:58:52",
-  "source_file_size": 401272,
-  "generation_date": "2024-10-28T20:58:57",
+  "source_file_date": "2024-11-07T15:54:25",
+  "source_file_size": 402910,
+  "generation_date": "2024-11-07T15:54:33",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/biolink_model.context.jsonld",