From ee84805bdf529f5de1b76ccc2070b887d61d3cd8 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Tue, 6 Apr 2021 15:28:22 -0700 Subject: [PATCH] update urls, phenotype_of predicate for mydisease phenotypicFeature -> Disease --- onehop/test_triples/KP/Service_Provider/MyChem.info_API.json | 3 +-- onehop/test_triples/KP/Service_Provider/MyGene.info_API.json | 3 +-- .../KP/Service_Provider/Ontology_Lookup_Service_API.json | 3 +-- onehop/test_triples/KP/Service_Provider/OpenTarget_API.json | 3 +-- onehop/test_triples/KP/Service_Provider/OpenTarget_README.md | 4 +++- onehop/test_triples/KP/Service_Provider/README.md | 2 +- .../test_triples/KP/Service_Provider/mydisease.info_API.json | 5 ++--- 7 files changed, 10 insertions(+), 13 deletions(-) diff --git a/onehop/test_triples/KP/Service_Provider/MyChem.info_API.json b/onehop/test_triples/KP/Service_Provider/MyChem.info_API.json index 659ae64..2e802ed 100644 --- a/onehop/test_triples/KP/Service_Provider/MyChem.info_API.json +++ b/onehop/test_triples/KP/Service_Provider/MyChem.info_API.json @@ -1,6 +1,5 @@ { - "url": "https://smart-api.info/ui/dc91716f44207d2e1287c727f281d339#/1.0.0/querySmartAPI", - "smartAPI_ID": "8f08d1446e0bb9c2b323713ce83e2bd3", + "url": "https://api.bte.ncats.io/v1/smartapi/8f08d1446e0bb9c2b323713ce83e2bd3/query", "TRAPI": true, "edges": [ { diff --git a/onehop/test_triples/KP/Service_Provider/MyGene.info_API.json b/onehop/test_triples/KP/Service_Provider/MyGene.info_API.json index e72107a..5f75e7f 100644 --- a/onehop/test_triples/KP/Service_Provider/MyGene.info_API.json +++ b/onehop/test_triples/KP/Service_Provider/MyGene.info_API.json @@ -1,6 +1,5 @@ { - "url": "https://smart-api.info/ui/dc91716f44207d2e1287c727f281d339#/1.0.0/querySmartAPI", - "smartAPI_ID": "59dce17363dce279d389100834e43648", + "url": "https://api.bte.ncats.io/v1/smartapi/59dce17363dce279d389100834e43648/query", "TRAPI": true, "edges": [ { diff --git a/onehop/test_triples/KP/Service_Provider/Ontology_Lookup_Service_API.json b/onehop/test_triples/KP/Service_Provider/Ontology_Lookup_Service_API.json index 0976871..1f86de7 100644 --- a/onehop/test_triples/KP/Service_Provider/Ontology_Lookup_Service_API.json +++ b/onehop/test_triples/KP/Service_Provider/Ontology_Lookup_Service_API.json @@ -1,6 +1,5 @@ { - "url": "https://smart-api.info/ui/dc91716f44207d2e1287c727f281d339#/1.0.0/querySmartAPI", - "smartAPI_ID": "1c056ffc7ed0dd1229e71c4752239465", + "url": "https://api.bte.ncats.io/v1/smartapi/1c056ffc7ed0dd1229e71c4752239465/query", "TRAPI": true, "edges": [ { diff --git a/onehop/test_triples/KP/Service_Provider/OpenTarget_API.json b/onehop/test_triples/KP/Service_Provider/OpenTarget_API.json index 9bff47c..0229717 100644 --- a/onehop/test_triples/KP/Service_Provider/OpenTarget_API.json +++ b/onehop/test_triples/KP/Service_Provider/OpenTarget_API.json @@ -1,6 +1,5 @@ { - "url": "https://smart-api.info/ui/dc91716f44207d2e1287c727f281d339#/1.0.0/querySmartAPI", - "smartAPI_ID": "542ba165e1b4227854cf7c0a8addcc79", + "url": "https://api.bte.ncats.io/v1/smartapi/542ba165e1b4227854cf7c0a8addcc79/query", "TRAPI": true, "edges": [ { diff --git a/onehop/test_triples/KP/Service_Provider/OpenTarget_README.md b/onehop/test_triples/KP/Service_Provider/OpenTarget_README.md index cd8442c..a7248b9 100644 --- a/onehop/test_triples/KP/Service_Provider/OpenTarget_README.md +++ b/onehop/test_triples/KP/Service_Provider/OpenTarget_README.md @@ -10,4 +10,6 @@ parameters: One of the answers should be EVEROLIMUS, which has ``` data.drug.id: "http://identifiers.org/chembl.compound/CHEMBL1908360" -``` \ No newline at end of file +``` + +Note: BTE TRAPI is currently having an issue. The raw output of this API is very redundant, and it seems that this is causing issues with the results section of the response (nodes and edges are fine). \ No newline at end of file diff --git a/onehop/test_triples/KP/Service_Provider/README.md b/onehop/test_triples/KP/Service_Provider/README.md index cb4d429..88ec2d7 100644 --- a/onehop/test_triples/KP/Service_Provider/README.md +++ b/onehop/test_triples/KP/Service_Provider/README.md @@ -1,4 +1,4 @@ -The JSON files assume that these APIs will be queried through BTE's TRAPI endpoint for querying individual SmartAPIs. They therefore include the url for the BTE endpoint, and the SmartAPI ID for the actual SmartAPI. The edge to the answer/object node should have an "api" attribute, with the name of the SmartAPI as the value. +The JSON files assume that these APIs will be queried through BTE's TRAPI endpoint for querying individual SmartAPIs (accessible through the URLs provided). Notes: - tests are also described as queries that can be made directly to the API, in the additional README files. Notice that many API endpoints do not handle curies (ID prefixes) or predicates. The format of these queries is specified by the x-bte-annotated endpoint in the SmartAPI registry file. diff --git a/onehop/test_triples/KP/Service_Provider/mydisease.info_API.json b/onehop/test_triples/KP/Service_Provider/mydisease.info_API.json index 55ad58f..c004cca 100644 --- a/onehop/test_triples/KP/Service_Provider/mydisease.info_API.json +++ b/onehop/test_triples/KP/Service_Provider/mydisease.info_API.json @@ -1,6 +1,5 @@ { - "url": "https://smart-api.info/ui/dc91716f44207d2e1287c727f281d339#/1.0.0/querySmartAPI", - "smartAPI_ID": "671b45c0301c8624abbd26ae78449ca2", + "url": "https://api.bte.ncats.io/v1/smartapi/671b45c0301c8624abbd26ae78449ca2/query", "TRAPI": true, "edges": [ { @@ -48,7 +47,7 @@ { "subject_category": "biolink:PhenotypicFeature", "object_category": "biolink:Disease", - "predicate": "biolink:related_to", + "predicate": "biolink:phenotype_of", "subject": "HP:0000224", "object": "MONDO:0012107" },