search

monarch-initiative / monarch-app

Monarch Initiative website and API
https://monarchinitiative.org/
BSD 3-Clause "New" or "Revised" License
18 stars 6 forks source link

STRING is an aggregator #393

Closed sagehrke closed 1 year ago

sagehrke commented 1 year ago

Physical interactions appear to come from STRING, but STRING is an aggregator. Shouldn’t a primary curated data source like BioGRID or Intact be ingested? This would also allow the inclusion of primary publications (currently blank).

Harry Caufield: Worth noting that primary source PMIDs can also be retrieved from STRING

sagehrke commented 1 year ago

Review STRING ingest. Provide evidence the data is being passed through STRING or curated from BioGRID or Intact. Action: (1) Provide better provenance. (2) See if we can find evidence.

RichardBruskiewich commented 1 year ago

Curating the primary knowledge source and publications can be done in the future; for the short term, we will add 'Evidence & Conclusion" codes to STRING edges, for all evidence categories with scores greater than zero

RichardBruskiewich commented 1 year ago

Partially resolved by https://github.com/monarch-initiative/monarch-ingest/pull/528.

monicacecilia commented 1 year ago

https://github.com/monarch-initiative/monarch-ingest/issues/533

kevinschaper commented 1 year ago

I'm inclined to close this and make a new issue for creating a BioGRID ingest

RichardBruskiewich commented 1 year ago

OK. Did Harry tell you where the STRING PMID's are lurking?

sagehrke commented 1 year ago

Closing. The BioGRID ingest is a different issue. Thank you!

caufieldjh commented 1 year ago

OK. Did Harry tell you where the STRING PMID's are lurking?

For reference, these can be retrieved from the evidence portion of the STRING Postgres DB (as per here: https://stringdb-downloads.org/download/database.schema.v12.0.pdf) - and individually through their API (https://string-db.org/help/api/)