Remove retracted publications in data flow

[kltm]

Project link

https://github.com/orgs/geneontology/projects/153

Project description

Add a QC check for annotations to retracted publications. Currently listed as gorule-0000022.

PI

Chris

Product owner (PO)

Pascale

Technical lead (TL)

Anushya

Other personnel (OP)

Seth, Dustin? (TBD)

Technical specs

TBD (template: https://docs.google.com/document/d/111UqtS3G0aJZpAijZYI3Da0t94OQpGePlPJsqZE4Tio/edit)

Other comments

N/A

[kltm]

Things to be worked out in discussion:

• [ ] what is the source< br / > @kltm to confirm (or not) eutils; fallback to europmc
• [ ] what format is the source
  line per pub; done
• [ ] where will we "cache" the source
  GH; go-site metadata/ (20k); retracted-publications.txt
• [ ] Add README for how to process and update file
• [ ] what is the update frequency of the source
  manually at first
• [ ] where does the source get used, specifically (i.e. as an optional CLI arg to ontobio)
  purpose: as some may not want to use ontobio w/this, it needs to be default optional (@mugitty to talk to @dustine32)
• [ ] how does the source get used, specifically (i.e. read into memory for each GAF/GPAD process)
  as above
• [ ] does this affect runtime (as per-line; doubtful, as likely hash lookup or something, but something to be mindful of)
  we'll default to: this is not likely to be a problem

[kltm]

Tagging @pgaudet and @mugitty; will discuss on Wednesday.

[kltm]

Closing out project; will just follow up as ticket: https://github.com/geneontology/go-site/issues/676