Update sources for KG2.7.7 - Githubissues

RTXteam / RTX-KG2

Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)

MIT License

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Update sources for KG2.7.7 #220

Closed acevedol closed 1 year ago

acevedol commented 2 years ago

Check and update all relevant upstream sources:

[x] SemMedDB: 43 (2021) - No change needed
[x] UMLS: 2020AA to UMLS: 2022AA
[x] ChEMBL: 27 to ChEMBL: 30
[x] DrugBank: 5.1 to Drugbank: 5.1.9
[x] Ensembl: 103 to Ensembl: 106
[x] GO annotations: 2021-11-08 to GO: 2022-07-01
[x] UniProtKB: 2021_04 to UniProtKB: 2022_02
[x] UniChem: 385 - No change needed
[x] DrugCentral: 48
[x] KEGG: 101.0 to 103.0

acevedol commented 2 years ago

SemMedDB made changes to their database schema since 2.0.

The existing extract-semmed.sh says version 43 but the list on kg2-versions.md says 23. Not sure why there's a discrepancy.

acevedol commented 2 years ago

SemMed version 43 is the correct current version of the DB. No changes needed at this time.

acevedol commented 2 years ago

Waiting for download approval for Drugbank

acevedol commented 2 years ago

It appears that GO and UniProt are supposed to get the most up-to-date release when they are extracted. I need to verify that is correct on the next build.

acevedol commented 2 years ago

KEGG queries an API to create a flat file, so I think it should get the latest release upon full build, but I will need to verify that.

acevedol commented 2 years ago

Finally got download approval for drugbank! Added drugbank_5.1.9.xml.gz to S3 bucket