search

geneontology / go-site

A collection of metadata, tools, and files associated with the Gene Ontology public web presence.
http://geneontology.org
BSD 3-Clause "New" or "Revised" License
43 stars 89 forks source link

Filtered goa_uniprot_all_noiea.gaf file does not contain any kind of header; add "edited" header comment to goa_uniprot_all.gaf #1753

Open kltm opened 2 years ago

kltm commented 2 years ago

In the release pipeline, the filtered noiea product of the goa_uniprot_all.gaf does not have a header. Minimally, it should have !gaf-version: 2.2; ideally, the usual pass-through notice (although that's handled by ontobio which we do not use here).

My guess is that the filter script is literally line matching based on species. I suspect adding a comment pass-through for the filter would fix this. As well, literally doing something like echo, cat, rm, and mv.

I'd also note that this would go away naturally with the species reorientation.

From https://github.com/geneontology/helpdesk/discussions/361

kltm commented 1 year ago

This is data (format) integrity.

kltm commented 1 year ago

Also, from @cmungall : add a comment to goa_uniprot_all that we are filtering the "canonical species" list and that this has been processed from the upstream.