remove conflicts

biolink · Nov 28, 2023 · 39d6b92 · 39d6b92
2 parents e2a4aef + a68e5bb
commit 39d6b92
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Showing 15 changed files with 43,470 additions and 18,458 deletions.
diff --git a/biolink-model.ttl b/biolink-model.ttl
diff --git a/biolink-model.yaml b/biolink-model.yaml
@@ -1500,13 +1500,6 @@ slots:
       sense in the full statement reading  (because “Chemical X affects increased expression of Gene Y'' is not 
       what we mean to say here: it causes increased expression of Gene Y)
 
-  qualifier:
-    is_a: association slot
-    description: >- 
-      grouping slot for all qualifiers on an edge.  useful for testing compliance with association classes
-    in_subset:
-      - translator_minimal
-
   statement qualifier:
     is_a: qualifier
     description: >-
@@ -5178,6 +5171,13 @@ slots:
     description: >-
       any slot that relates an association to another entity
 
+  qualifier:
+    is_a: association slot
+    description: >- 
+      grouping slot for all qualifiers on an edge.  useful for testing compliance with association classes
+    in_subset:
+      - translator_minimal
+
   original subject:
     is_a: association slot
     description: >-

diff --git a/project/jsonld/biolink-model.context.jsonld b/project/jsonld/biolink-model.context.jsonld
@@ -1,11 +1,15 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
+<<<<<<< HEAD:project/jsonld/biolink-model.context.jsonld
 <<<<<<< HEAD:project/jsonld/biolink-model.context.jsonld
       "generation_date": "2023-11-07T09:12:32",
 =======
       "generation_date": "2023-11-10T19:23:25",
 >>>>>>> master:context.jsonld
+=======
+      "generation_date": "2023-11-25T17:56:50",
+>>>>>>> master:contextn.jsonld
       "source": "biolink-model.yaml"
    },
    "@context": {

diff --git a/project/jsonld/biolink_model.context.jsonld b/project/jsonld/biolink_model.context.jsonld
@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2023-11-27T13:10:28",
+      "generation_date": "2023-11-27T16:02:18",
       "source": "biolink_model.yaml"
    },
    "@context": {

diff --git a/project/jsonld/biolink_model.jsonld b/project/jsonld/biolink_model.jsonld
@@ -3808,7 +3808,7 @@
       "definition_uri": "https://w3id.org/biolink/vocab/direction_qualifier",
       "description": "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree.",
       "notes": [
-        "the qualifier \u2018increased\u2019 combines with a core concept of \u2018Gene X\u2019 and an aspect of \u2018expression\u2019 to express the composed concept \u2018increased expression of Gene X\u2019    the qualifier \u2018decreased\u2019 combines with a core concept of \u2018Protein X\u2019 and an aspect of \u2018abundance\u2019 to express the composed concept \u2018decreased abundance of Protein X\u2019"
+        "the qualifier \u2018increased\u2019 combines with a core concept of \u2018Gene X\u2019 and an aspect of \u2018expression\u2019 to express the  composed concept \u2018increased expression of Gene X\u2019    the qualifier \u2018decreased\u2019 combines with a core concept of \u2018Protein X\u2019 and an aspect of \u2018abundance\u2019 to  express the composed concept \u2018decreased abundance of Protein X\u2019"
       ],
       "in_subset": [
         "translator_minimal"
@@ -3985,6 +3985,7 @@
     {
       "name": "subject_direction_qualifier",
       "definition_uri": "https://w3id.org/biolink/vocab/subject_direction_qualifier",
+      "description": "A qualifier that composes with a core subject concept to describe a change in its direction or degree.",
       "in_subset": [
         "translator_minimal"
       ],
@@ -4100,6 +4101,7 @@
     {
       "name": "object_direction_qualifier",
       "definition_uri": "https://w3id.org/biolink/vocab/object_direction_qualifier",
+      "description": "A qualifier that composes with a core object concept to describe a change in its direction or degree.",
       "in_subset": [
         "translator_minimal"
       ],
@@ -4136,21 +4138,6 @@
       "range": "string",
       "@type": "SlotDefinition"
     },
-    {
-      "name": "qualifier",
-      "definition_uri": "https://w3id.org/biolink/vocab/qualifier",
-      "description": "grouping slot for all qualifiers on an edge.  useful for testing compliance with association classes",
-      "in_subset": [
-        "translator_minimal"
-      ],
-      "from_schema": "https://w3id.org/biolink/biolink-model",
-      "is_a": "association_slot",
-      "domain": "Association",
-      "slot_uri": "https://w3id.org/biolink/vocab/qualifier",
-      "owner": "qualifier",
-      "range": "string",
-      "@type": "SlotDefinition"
-    },
     {
       "name": "statement_qualifier",
       "definition_uri": "https://w3id.org/biolink/vocab/statement_qualifier",
@@ -10896,6 +10883,21 @@
       "range": "string",
       "@type": "SlotDefinition"
     },
+    {
+      "name": "qualifier",
+      "definition_uri": "https://w3id.org/biolink/vocab/qualifier",
+      "description": "grouping slot for all qualifiers on an edge.  useful for testing compliance with association classes",
+      "in_subset": [
+        "translator_minimal"
+      ],
+      "from_schema": "https://w3id.org/biolink/biolink-model",
+      "is_a": "association_slot",
+      "domain": "Association",
+      "slot_uri": "https://w3id.org/biolink/vocab/qualifier",
+      "owner": "qualifier",
+      "range": "string",
+      "@type": "SlotDefinition"
+    },
     {
       "name": "original_subject",
       "definition_uri": "https://w3id.org/biolink/vocab/original_subject",
@@ -16111,6 +16113,7 @@
     {
       "name": "chemical_affects_gene_association_subject_direction_qualifier",
       "definition_uri": "https://w3id.org/biolink/vocab/subject_direction_qualifier",
+      "description": "A qualifier that composes with a core subject concept to describe a change in its direction or degree.",
       "in_subset": [
         "translator_minimal"
       ],
@@ -16310,6 +16313,7 @@
     {
       "name": "chemical_affects_gene_association_object_direction_qualifier",
       "definition_uri": "https://w3id.org/biolink/vocab/object_direction_qualifier",
+      "description": "A qualifier that composes with a core object concept to describe a change in its direction or degree.",
       "in_subset": [
         "translator_minimal"
       ],
@@ -16536,6 +16540,7 @@
     {
       "name": "gene_affects_chemical_association_subject_direction_qualifier",
       "definition_uri": "https://w3id.org/biolink/vocab/subject_direction_qualifier",
+      "description": "A qualifier that composes with a core subject concept to describe a change in its direction or degree.",
       "in_subset": [
         "translator_minimal"
       ],
@@ -16754,6 +16759,7 @@
     {
       "name": "gene_affects_chemical_association_object_direction_qualifier",
       "definition_uri": "https://w3id.org/biolink/vocab/object_direction_qualifier",
+      "description": "A qualifier that composes with a core object concept to describe a change in its direction or degree.",
       "in_subset": [
         "translator_minimal"
       ],
@@ -18084,6 +18090,7 @@
     {
       "name": "gene_to_disease_or_phenotypic_feature_association_object_direction_qualifier",
       "definition_uri": "https://w3id.org/biolink/vocab/object_direction_qualifier",
+      "description": "A qualifier that composes with a core object concept to describe a change in its direction or degree.",
       "in_subset": [
         "translator_minimal"
       ],
@@ -21007,6 +21014,7 @@
     {
       "name": "chemical_entity_or_gene_or_gene_product_regulates_gene_association_object_direction_qualifier",
       "definition_uri": "https://w3id.org/biolink/vocab/object_direction_qualifier",
+      "description": "A qualifier that composes with a core object concept to describe a change in its direction or degree.",
       "in_subset": [
         "translator_minimal"
       ],
@@ -33383,9 +33391,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "biolink_model.yaml",
-  "source_file_date": "2023-11-27T13:10:21",
-  "source_file_size": 366864,
-  "generation_date": "2023-11-27T13:10:30",
+  "source_file_date": "2023-11-27T16:02:11",
+  "source_file_size": 367135,
+  "generation_date": "2023-11-27T16:02:21",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/biolink_model.context.jsonld",

diff --git a/project/jsonschema/biolink_model.schema.json b/project/jsonschema/biolink_model.schema.json
@@ -2919,7 +2919,8 @@
                     "type": "array"
                 },
                 "object_direction_qualifier": {
-                    "$ref": "#/$defs/DirectionQualifierEnum"
+                    "$ref": "#/$defs/DirectionQualifierEnum",
+                    "description": "A qualifier that composes with a core object concept to describe a change in its direction or degree."
                 },
                 "object_label_closure": {
                     "description": "Used to hold the object label closure of an association. This is a denormalized  field used primarily in the SQL serialization of a knowledge graph via KGX.",
@@ -4025,7 +4026,8 @@
                     "$ref": "#/$defs/ChemicalEntityDerivativeEnum"
                 },
                 "subject_direction_qualifier": {
-                    "$ref": "#/$defs/DirectionQualifierEnum"
+                    "$ref": "#/$defs/DirectionQualifierEnum",
+                    "description": "A qualifier that composes with a core subject concept to describe a change in its direction or degree."
                 },
                 "subject_form_or_variant_qualifier": {
                     "$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum"
@@ -4459,7 +4461,8 @@
                     "type": "array"
                 },
                 "object_direction_qualifier": {
-                    "$ref": "#/$defs/DirectionQualifierEnum"
+                    "$ref": "#/$defs/DirectionQualifierEnum",
+                    "description": "A qualifier that composes with a core object concept to describe a change in its direction or degree."
                 },
                 "object_label_closure": {
                     "description": "Used to hold the object label closure of an association. This is a denormalized  field used primarily in the SQL serialization of a knowledge graph via KGX.",
@@ -8144,7 +8147,8 @@
                     "type": "array"
                 },
                 "object_direction_qualifier": {
-                    "$ref": "#/$defs/DirectionQualifierEnum"
+                    "$ref": "#/$defs/DirectionQualifierEnum",
+                    "description": "A qualifier that composes with a core object concept to describe a change in its direction or degree."
                 },
                 "object_label_closure": {
                     "description": "Used to hold the object label closure of an association. This is a denormalized  field used primarily in the SQL serialization of a knowledge graph via KGX.",
@@ -10722,7 +10726,8 @@
                     "type": "array"
                 },
                 "object_direction_qualifier": {
-                    "$ref": "#/$defs/DirectionQualifierEnum"
+                    "$ref": "#/$defs/DirectionQualifierEnum",
+                    "description": "A qualifier that composes with a core object concept to describe a change in its direction or degree."
                 },
                 "object_label_closure": {
                     "description": "Used to hold the object label closure of an association. This is a denormalized  field used primarily in the SQL serialization of a knowledge graph via KGX.",
@@ -13360,7 +13365,8 @@
                     "type": "string"
                 },
                 "subject_direction_qualifier": {
-                    "$ref": "#/$defs/DirectionQualifierEnum"
+                    "$ref": "#/$defs/DirectionQualifierEnum",
+                    "description": "A qualifier that composes with a core subject concept to describe a change in its direction or degree."
                 },
                 "subject_form_or_variant_qualifier": {
                     "$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum"
@@ -13506,7 +13512,8 @@
                     "type": "array"
                 },
                 "object_direction_qualifier": {
-                    "$ref": "#/$defs/DirectionQualifierEnum"
+                    "$ref": "#/$defs/DirectionQualifierEnum",
+                    "description": "A qualifier that composes with a core object concept to describe a change in its direction or degree."
                 },
                 "object_label_closure": {
                     "description": "Used to hold the object label closure of an association. This is a denormalized  field used primarily in the SQL serialization of a knowledge graph via KGX.",
@@ -13834,7 +13841,8 @@
                     "type": "array"
                 },
                 "object_direction_qualifier": {
-                    "$ref": "#/$defs/DirectionQualifierEnum"
+                    "$ref": "#/$defs/DirectionQualifierEnum",
+                    "description": "A qualifier that composes with a core object concept to describe a change in its direction or degree."
                 },
                 "object_label_closure": {
                     "description": "Used to hold the object label closure of an association. This is a denormalized  field used primarily in the SQL serialization of a knowledge graph via KGX.",
@@ -14137,7 +14145,8 @@
                     "type": "array"
                 },
                 "object_direction_qualifier": {
-                    "$ref": "#/$defs/DirectionQualifierEnum"
+                    "$ref": "#/$defs/DirectionQualifierEnum",
+                    "description": "A qualifier that composes with a core object concept to describe a change in its direction or degree."
                 },
                 "object_label_closure": {
                     "description": "Used to hold the object label closure of an association. This is a denormalized  field used primarily in the SQL serialization of a knowledge graph via KGX.",
@@ -14366,7 +14375,8 @@
                     "type": "array"
                 },
                 "object_direction_qualifier": {
-                    "$ref": "#/$defs/DirectionQualifierEnum"
+                    "$ref": "#/$defs/DirectionQualifierEnum",
+                    "description": "A qualifier that composes with a core object concept to describe a change in its direction or degree."
                 },
                 "object_label_closure": {
                     "description": "Used to hold the object label closure of an association. This is a denormalized  field used primarily in the SQL serialization of a knowledge graph via KGX.",
@@ -15963,7 +15973,8 @@
                     "type": "array"
                 },
                 "object_direction_qualifier": {
-                    "$ref": "#/$defs/DirectionQualifierEnum"
+                    "$ref": "#/$defs/DirectionQualifierEnum",
+                    "description": "A qualifier that composes with a core object concept to describe a change in its direction or degree."
                 },
                 "object_label_closure": {
                     "description": "Used to hold the object label closure of an association. This is a denormalized  field used primarily in the SQL serialization of a knowledge graph via KGX.",
@@ -25854,7 +25865,8 @@
                     "type": "string"
                 },
                 "object_direction_qualifier": {
-                    "$ref": "#/$defs/DirectionQualifierEnum"
+                    "$ref": "#/$defs/DirectionQualifierEnum",
+                    "description": "A qualifier that composes with a core object concept to describe a change in its direction or degree."
                 },
                 "object_form_or_variant_qualifier": {
                     "type": "string"
@@ -25884,7 +25896,8 @@
                     "type": "string"
                 },
                 "subject_direction_qualifier": {
-                    "$ref": "#/$defs/DirectionQualifierEnum"
+                    "$ref": "#/$defs/DirectionQualifierEnum",
+                    "description": "A qualifier that composes with a core subject concept to describe a change in its direction or degree."
                 },
                 "subject_form_or_variant_qualifier": {
                     "type": "string"