Projects update meeting 2023-12-13

Attendees

• Members: Kimberly, Pascale, Seth, Suzi, Jim, Huaiyu, Paul, Chris, Cynthia
• Present:

Announcements

• Do people want to meet next week ? (Dec 20th) - or are people out already?
• Next call will be January 10th.

Projects status

https://github.com/orgs/geneontology/projects/108/views/1

Discussion topics

Pipeline issues

Snapshot has not run since Nov 6th, more and more issues. Possible solutions?

• https://github.com/geneontology/pipeline/issues/316
• https://github.com/geneontology/pipeline/issues/349

GPAD specs

• Official specs: https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md
• GO website documentation: https://github.com/geneontology/geneontology.github.io/blob/master/_docs/gene-product-association-data-gpad-format-20.md

Questions

• Who is the target audience for each of the 2 documents? We should write who is concerned
• In 'official specs', if we have values listed (like relations), are these part of the specs? If they are, should we move them to a different location, to allow some flexibility?
• Interacting taxon as an extension rather than as its own file?
• GO version recommendation:
  • website has go-version: https://doi.org/10.5281/zenodo.8436609
  • official specs have http://purl.obolibrary.org/obo/go/releases/2023-10-09/go.owl
    • what if people use go-plus or another version of the ontology?

Slims versus ribbons

Pascale

UniProt request:

• it would be nice to have one 'ribbon' subset for various taxonomic range: animals, plants, cellular eukaryotes, bacteria and viruses
• it would be easier if these were named using a same pattern, for eg. 'go-ribbon-x'; or maybe we could add some text in file headers?

User requests

Suzi

• neuropathology helpdesk question
• twitter post about women’s health

AmiGO now showing reaction participants

• See https://amigo.geneontology.org/amigo/term/GO:0018812#display-lineage-tab
• Should we show other relations? inputs/outputs, Uberon, CL... ?