NCATS-Tangerine · colleenXu · Jun 14, 2024 · Mar 4, 2024 · Mar 4, 2024 · Mar 4, 2024
diff --git a/AGR/agr.yaml b/AGR/agr.yaml
@@ -16,7 +16,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "3.5.3"
+    biolink-version: "4.1.6"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/agr

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: "3.5.0"
+    biolink-version: "4.1.6"
     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: "3.5.0"
+    biolink-version: "4.1.6"
 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: "3.5.0"
+    biolink-version: "4.1.6"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/ebigene2phenotype

diff --git a/MGIgene2phenotype/smartapi.yaml b/MGIgene2phenotype/smartapi.yaml
@@ -19,7 +19,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "3.5.0"
+    biolink-version: "4.1.6"
 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: "3.5.0"
+    biolink-version: "4.1.6"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/bindingdb

diff --git a/biolink/openapi.yml b/biolink/openapi.yml
@@ -19,7 +19,7 @@ info:
     team:
     - "Service Provider"
     - "Standards Reference Implementation Team"  
-    biolink-version: "3.5.3"
+    biolink-version: "4.1.6"
 servers:
 - description: Production server
   url: https://api-v3.monarchinitiative.org

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: "3.5.0"
+    biolink-version: "4.1.6"
 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: "3.5.0"
+    biolink-version: "4.1.6"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/bioplanet_pathway_gene

diff --git a/biothings_explorer/service-provider-trapi.yaml b/biothings_explorer/service-provider-trapi.yaml
@@ -18,7 +18,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "3.5.3"
+    biolink-version: "4.1.6"
     infores: "infores:service-provider-trapi"
   x-trapi:
     version: 1.4.0

diff --git a/biothings_explorer/smartapi.yaml b/biothings_explorer/smartapi.yaml
@@ -12,7 +12,7 @@ info:
     component: ARA
     team:
       - Exploring Agent
-    biolink-version: "3.5.3"
+    biolink-version: "4.1.6"
     infores: "infores:biothings-explorer"
   x-trapi:
     version: 1.4.0

diff --git a/biothings_foodb/smartapi.yaml b/biothings_foodb/smartapi.yaml
@@ -16,7 +16,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "3.5.3"
+    biolink-version: "4.1.6"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/foodb

diff --git a/complexportal/smartapi.yaml b/complexportal/smartapi.yaml
@@ -15,7 +15,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "3.5.3"
+    biolink-version: "4.1.6"
 servers:
 - url: https://www.ebi.ac.uk/intact/complex-ws
   description: Production server

diff --git a/ddinter/ddinter.yaml b/ddinter/ddinter.yaml
@@ -16,7 +16,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "3.5.0"
+    biolink-version: "4.1.6"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/ddinter

diff --git a/dgidb/openapi.yml b/dgidb/openapi.yml
@@ -16,7 +16,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "3.5.0"
+    biolink-version: "4.1.6"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/dgidb

diff --git a/ebi_proteins/openapi.yml b/ebi_proteins/openapi.yml
@@ -18,7 +18,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "3.5.0"
+    biolink-version: "4.1.6"
 servers:
   - url: 'https://www.ebi.ac.uk/proteins/api'
     x-maturity: production

diff --git a/fooddata_central/smartapi.yaml b/fooddata_central/smartapi.yaml
@@ -17,7 +17,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "3.5.3"
+    biolink-version: "4.1.6"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/fooddata

diff --git a/go_bp/smartapi.yaml b/go_bp/smartapi.yaml
@@ -16,7 +16,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "3.5.0"
+    biolink-version: "4.1.6"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/go_bp

diff --git a/go_cc/smartapi.yaml b/go_cc/smartapi.yaml
@@ -16,7 +16,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "3.5.0"
+    biolink-version: "4.1.6"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/go_cc

diff --git a/go_mf/smartapi.yaml b/go_mf/smartapi.yaml
@@ -16,7 +16,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "3.5.0"
+    biolink-version: "4.1.6"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/go_mf

diff --git a/gtrx/gtrx.yaml b/gtrx/gtrx.yaml
@@ -19,7 +19,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "3.5.0"
+    biolink-version: "4.1.6"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/gtrx
@@ -574,6 +574,7 @@ components:
   ## 2 potential types:
   ## - Disease: OMIM ID without prefixes in subject.omim
   ## - SmallMolecule: UNII ID without prefix in object.intervention.inxight
+  ## keeping predicates as treats/treated_by because these are curated, recommended interventions by experts 
   ## 695 records total
   ## knowledge_level / agent_type: highly curated, see Fig.2 and Methods of https://www.nature.com/articles/s41467-022-31446-6#Sec2
     disease-drug:

diff --git a/hpo/smartapi.yaml b/hpo/smartapi.yaml
@@ -15,7 +15,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "3.5.3"
+    biolink-version: "4.1.6"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/hpo

diff --git a/iPTMnet/smartapi.yaml b/iPTMnet/smartapi.yaml
@@ -15,7 +15,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "3.5.3"
+    biolink-version: "4.1.6"
 servers:
 - description: Encrypted Production server
   url: https://research.bioinformatics.udel.edu/iptmnet/api

diff --git a/idisk/smartapi.yaml b/idisk/smartapi.yaml
@@ -16,7 +16,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "3.5.0"
+    biolink-version: "4.1.6"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/idisk
@@ -773,7 +773,6 @@ components:
     is_effective_for:
     ## there are 654 records with the is_effective_for field 
     ##   most use NMCD (552), but some use MSKCC (238). Some records must have both?
-    ## the dietary supplement is said to treat disease/condition or may be used for it...
     - supportBatch: true
       useTemplating: true ## flag to say templating is being used below
       inputs:
@@ -795,7 +794,8 @@ components:
         # fields: is_effective_for.umls,is_effective_for.source.name
         fields: is_effective_for.umls
         size: 1000  ## size limit; just in case
-      predicate: treats  ## closest biolink predicate?
+      ## the dietary supplement is said to treat disease/condition or may be used for it...
+      predicate: applied_to_treat
       source: "infores:idisk"
       knowledge_level: knowledge_assertion
       agent_type: automated_agent
@@ -822,7 +822,7 @@ components:
       parameters:
         fields: umls
         size: 1000  ## note size limit
-      predicate: treated_by
+      predicate: treatment_applications_from
       source: "infores:idisk"
       knowledge_level: knowledge_assertion
       agent_type: automated_agent

diff --git a/innatedb/smartapi.yaml b/innatedb/smartapi.yaml
@@ -19,7 +19,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "3.5.3"
+    biolink-version: "4.1.6"
 servers:
 - description: Encrypted Production server
   url: https://biothings.ncats.io/innatedb

diff --git a/litvar/smartapi.yaml b/litvar/smartapi.yaml
@@ -18,7 +18,7 @@ info:
     component: KP
     team:
       - Service Provider
-    biolink-version: "3.5.0"
+    biolink-version: "4.1.6"
 servers:
 - url: https://www.ncbi.nlm.nih.gov/research/bionlp/litvar/api/v1
   description: Production server