From a053458b965169265f3bec01cd35c2bd73e670d7 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Tue, 22 Oct 2024 11:42:36 -0700 Subject: [PATCH 1/4] chore: update api list to current main version --- config/api_list.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/config/api_list.yaml b/config/api_list.yaml index e8430c8..b301ce4 100644 --- a/config/api_list.yaml +++ b/config/api_list.yaml @@ -126,10 +126,14 @@ include: # not accessible by team or api-specific endpoints - id: e51073371d7049b9643e1edbdd61bcbd name: Clinical Trials KP - TRAPI 1.5.0 + includeFlipped: true - id: edc04feaf16c12424737988ce2e90d60 name: Drug Approvals KP - TRAPI 1.5.0 + includeFlipped: true - id: a8be4ea3fe8fa80a952ead0b3c5e4bc1 name: Microbiome KP - TRAPI 1.5.0 + includeFlipped: true - id: 1b6de23ed3c4e0713b20794477ba1e39 name: Multiomics KP - TRAPI 1.5.0 + includeFlipped: true exclude: [] # if adding exclude remove these square brackets From 6503658491bf14ff1568135158d699ec1d67c00c Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Tue, 22 Oct 2024 11:43:11 -0700 Subject: [PATCH 2/4] feat: remove MolePro from use --- config/api_list.yaml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/config/api_list.yaml b/config/api_list.yaml index b301ce4..1f9cb44 100644 --- a/config/api_list.yaml +++ b/config/api_list.yaml @@ -118,10 +118,6 @@ include: # not accessible by team or api-specific endpoints - id: 412af63e15b73e5a30778aac84ce313f name: Connections Hypothesis Provider API - # TRAPI (Translator standard) APIs: Molecular Data Provider - # not accessible by team or api-specific endpoints - - id: 1901bab8d33bb70b124f400ec1cfdba3 - name: MolePro # TRAPI (Translator standard) APIs: Multiomics (made with RTX team Plover) # not accessible by team or api-specific endpoints - id: e51073371d7049b9643e1edbdd61bcbd From a8670cc5c173028e5ddb6ed2909a52d34305ea2e Mon Sep 17 00:00:00 2001 From: Jackson Callaghan <43009413+tokebe@users.noreply.github.com> Date: Tue, 22 Oct 2024 15:22:09 -0400 Subject: [PATCH 3/4] Revert "chore: add override for semmeddb" --- config/smartapi_overrides.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/config/smartapi_overrides.yaml b/config/smartapi_overrides.yaml index f1adf0b..a4bdda0 100644 --- a/config/smartapi_overrides.yaml +++ b/config/smartapi_overrides.yaml @@ -2,7 +2,6 @@ config: only_overrides: false apis: { - "1d288b3a3caf75d541ffaae3aab386c8": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/refs/heads/semmeddb_publication_refactor/semmeddb/smartapi.yaml", "8f08d1446e0bb9c2b323713ce83e2bd3": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/refs/heads/remove-clinical-trials/mychem.info/openapi_full.yml", "1138c3297e8e403b6ac10cff5609b319": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/refs/heads/remove-clinical-trials/repodb/smartapi.yaml", "edeb26858bd27d0322af93e7a9e08761": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/refs/heads/add-pfocr-IDnamespaces/pfocr/smartapi.yaml" From e200b5e4da37a59488cab556db486c9f373ee4b9 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Wed, 30 Oct 2024 19:36:57 -0700 Subject: [PATCH 4/4] feat: use individual automats, remove use of drug approvals --- config/api_list.yaml | 36 ++++++++++++++++++++++++++++++------ 1 file changed, 30 insertions(+), 6 deletions(-) diff --git a/config/api_list.yaml b/config/api_list.yaml index 1f9cb44..42673f7 100644 --- a/config/api_list.yaml +++ b/config/api_list.yaml @@ -102,9 +102,36 @@ include: name: Text Mining Targeted Association API # TRAPI (Translator standard) APIs: Automat # not accessible by team or api-specific endpoints - # using robokop to access all automat resources at once - - id: 4f9c8853b721ef1f14ecee6d92fc19b5 - name: Automat-robokop(Trapi v1.5.0) + # Notes: We don't ingest the following: + # - Automat-robokop: seems to repeat a lot of data that is in the other APIs + - id: f82c01b15c46e024212c1a3271aaef0b + name: Automat-ctd(Trapi v1.5.0) + - id: 673b9fc76973dfa5fe3ed151fdbfc807 + name: Automat-drug-central(Trapi v1.5.0) + - id: eef72049e4e01c020b7799f711e0e65b + name: Automat-gtex(Trapi v1.5.0) + - id: 759df287a21c30cd514df323be02a84b + name: Automat-gtopdb(Trapi v1.5.0) + - id: 349fed5531c094c33f10c071efe9d0de + name: Automat-gwas-catalog(Trapi v1.5.0) + - id: a5fe24f987331b58191e67598118f369 + name: Automat-hetionet(Trapi v1.5.0) + - id: 8671309d2b94e413a4c1f9a9f82e4660 + name: Automat-hgnc(Trapi v1.5.0) + - id: 0a1c0f46f4950b82b1aa7dad27aad10a + name: Automat-hmdb(Trapi v1.5.0) + - id: cb7a43d444cb3dcbe8e3c78d314334cf + name: Automat-human-goa(Trapi v1.5.0) + - id: c64d583402f21cc85810d33befe49c86 + name: Automat-icees-kg(Trapi v1.5.0) + - id: b4023595664163e0aec5e825da150e16 + name: Automat-intact(Trapi v1.5.0) + - id: 3f78d3fb8a7a577fbc7cc0a913ac3fc5 + name: Automat-panther(Trapi v1.5.0) + - id: 1f057c53d42694686369f0e542f965c6 + name: Automat-pharos(Trapi v1.5.0) + - id: 2aca41fc6c3dc426ec6583d42603be02 + name: Automat-viral-proteome(Trapi v1.5.0) # TRAPI (Translator standard) APIs: COHD # not accessible by team or api-specific endpoints # notes on COHD: @@ -123,9 +150,6 @@ include: - id: e51073371d7049b9643e1edbdd61bcbd name: Clinical Trials KP - TRAPI 1.5.0 includeFlipped: true - - id: edc04feaf16c12424737988ce2e90d60 - name: Drug Approvals KP - TRAPI 1.5.0 - includeFlipped: true - id: a8be4ea3fe8fa80a952ead0b3c5e4bc1 name: Microbiome KP - TRAPI 1.5.0 includeFlipped: true