Merge pull request #106 from NCATS-Tangerine/biolink3

qualifiers / biolink3 update
NCATS-Tangerine · Mar 16, 2023 · faae1a4 · faae1a4
2 parents 021cd57 + ec1da25
commit faae1a4
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Showing 37 changed files with 7,898 additions and 2,208 deletions.
diff --git a/CTD/smartapi.yaml b/CTD/smartapi.yaml
@@ -11,7 +11,7 @@ info:
     url: https://ctdbase.org/help/contact.go
   x-translator:
     infores: "infores:ctd"
-    biolink-version: "2.4.8"
+    biolink-version: "3.1.1"
     component: KP
     team:
       - Service Provider

diff --git a/DISEASES/smartapi.yaml b/DISEASES/smartapi.yaml
@@ -16,7 +16,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "2.2.13"
+    biolink-version: "3.1.1"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/DISEASES

diff --git a/EBIgene2phenotype/smartapi.yaml b/EBIgene2phenotype/smartapi.yaml
@@ -16,7 +16,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "2.2.13"
+    biolink-version: "3.1.1"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/ebigene2phenotype

diff --git a/MGIgene2phenotype/smartapi.yaml b/MGIgene2phenotype/smartapi.yaml
@@ -16,7 +16,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "2.2.13"
+    biolink-version: "3.1.1"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/mgigene2phenotype

diff --git a/bindingdb/smartapi.yaml b/bindingdb/smartapi.yaml
@@ -16,7 +16,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "2.4.8"
+    biolink-version: "3.1.1"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/bindingdb

diff --git a/biolink/openapi.yml b/biolink/openapi.yml
@@ -15,7 +15,7 @@ info:
     team:
     - "Service Provider"
     - "Standards Reference Implementation Team"  
-    biolink-version: "2.2.13"
+    biolink-version: "3.1.1"
 servers:
 - description: Production server
   url: https://api.monarchinitiative.org/api

diff --git a/bioplanet/bioplanet-pathway-disease.yaml b/bioplanet/bioplanet-pathway-disease.yaml
@@ -16,7 +16,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "2.2.13"
+    biolink-version: "3.1.1"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/bioplanet_pathway_disease

diff --git a/bioplanet/bioplanet-pathway-gene.yaml b/bioplanet/bioplanet-pathway-gene.yaml
@@ -17,7 +17,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "2.2.13"
+    biolink-version: "3.1.1"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/bioplanet_pathway_gene

diff --git a/biothings_explorer/qualifier-sri-test-service.json b/biothings_explorer/qualifier-sri-test-service.json
@@ -0,0 +1,75 @@
+{
+    "infores": "service-provider-trapi",
+    "edges": [
+        {
+            "underlying_api_infores": "biothings-dgidb",
+            "underlying_source_infores": "dgidb",
+            "subject_category": "biolink:SmallMolecule",
+            "subject_id": "CHEMBL.COMPOUND:CHEMBL266510",
+            "subject_name": "FLINDOKALNER",
+            "predicate": "biolink:affects",
+            "object_category": "biolink:Gene",
+            "object_id": "NCBIGene:9132",
+            "object_name": "KCNQ4",
+            "qualifiers": [
+                {
+                    "qualifier_type_id": "biolink:qualified_predicate",
+                    "qualifier_value": "biolink:causes"
+                },
+                {
+                    "qualifier_type_id": "biolink:object_aspect_qualifier",
+                    "qualifier_value": "activity"
+                },
+                {
+                    "qualifier_type_id": "biolink:object_direction_qualifier",
+                    "qualifier_value": "increased"
+                },
+                {
+                    "qualifier_type_id": "biolink:causal_mechanism_qualifier",
+                    "qualifier_value": "activation"
+                }
+            ]
+        },
+        {
+            "underlying_api_infores": "biothings-go-bp",
+            "underlying_source_infores": "go",
+            "subject_category": "biolink:BiologicalProcess",
+            "subject_id": "GO:0090272",
+            "subject_name": "negative regulation of fibroblast growth factor production",
+            "predicate": "biolink:regulates",
+            "object_category": "biolink:BiologicalProcess",
+            "object_id": "GO:0090269",
+            "object_name": "fibroblast growth factor production",
+            "qualifiers": [
+                {
+                    "qualifier_type_id": "biolink:object_direction_qualifier",
+                    "qualifier_value": "downregulated"
+                }
+            ]
+        },
+        {
+            "underlying_api_infores": "text-mining-provider-targeted",
+            "subject_category": "biolink:SmallMolecule",
+            "subject_id": "CHEBI:3215",
+            "subject_name": "bupivacaine",
+            "predicate": "biolink:affects",
+            "object_category": "biolink:Gene",
+            "object_id": "UniProtKB:Q9P2L0",
+            "object_name": "WDR35",
+            "qualifiers": [
+                {
+                    "qualifier_type_id": "biolink:qualified_predicate",
+                    "qualifier_value": "biolink:causes"
+                },
+                {
+                    "qualifier_type_id": "biolink:object_aspect_qualifier",
+                    "qualifier_value": "activity_or_abundance"
+                },
+                {
+                    "qualifier_type_id": "biolink:object_direction_qualifier",
+                    "qualifier_value": "increased"
+                }
+            ]
+        }
+    ]
+}
diff --git a/biothings_explorer/service-provider-trapi.yaml b/biothings_explorer/service-provider-trapi.yaml
@@ -36,7 +36,7 @@ info:
         - "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biothings_explorer/sri-test-text-mining.json"
   x-translator:
     infores: "infores:service-provider-trapi"
-    biolink-version: 2.4.8
+    biolink-version: "3.1.1"
     component: KP
     team:
       - Service Provider

diff --git a/biothings_explorer/smartapi.yaml b/biothings_explorer/smartapi.yaml
@@ -25,7 +25,7 @@ info:
         url: "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/5b19e854524c48a39125d545bec13f637661a09f/biothings_explorer/sri-test-bte-ara.json"
   x-translator:
     infores: "infores:biothings-explorer"
-    biolink-version: 2.4.8
+    biolink-version: "3.1.1"
     component: ARA
     team:
       - Exploring Agent

diff --git a/ddinter/ddinter.yaml b/ddinter/ddinter.yaml
@@ -16,7 +16,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "2.4.8"
+    biolink-version: "3.1.1"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/ddinter