Projects update meeting 2024-08-14
Attendees
- Members: Chris, Kimberly, Pascale, Seth, Suzi, Jim, Huaiyu, Paul, Cynthia
- Present: Chris, Kimberly, Seth, Suzi, Jim, Huaiyu
- Regrets: Paul, Pascale, Cynthia
Discussion points
Outstanding discussion points from last call
GPAD2.0 output from Minerva
- New task for Anushya?
- Decision: not a priority for now
We ask minerva to produce a GPAD- that immediate product is off-spec
There's a perl script that chops into MOD files, these go through Ontobio, and this is where the on-spec file comes from
Sierra's work means this first step is now on-spec, not exposing an off-spec product anymore. Alex is/was picking up the early file, now that the pipeline is broken up for Alex (who is now basically GO Central), there's an on-spec QC'd product available for Alex to pick up
K: This would be good for the fall meeting agenda
S: agreed, already working on a slide deck
- where to get certain information, de-duplication of effort
- getting GO-CAM QC up to par
Interontology links
- Are these in or out ?
- What does in or out mean? Cjm (talk) 20:34, 13 August 2024 (EDT)
- Is this F2P and propagation of annotations? E.g. https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-0000023.md
- or this one: https://github.com/geneontology/go-site/tree/master/metadata/rules#gorule0000062 (propagation within MF)
- What does in or out mean? Cjm (talk) 20:34, 13 August 2024 (EDT)
Punt until next meeting
EcoCyc links
EcoCyc expecting that we link back to them
- For context: https://github.com/geneontology/go-site/issues/1961
This would be straightforward.
Action: Ask Alex to produce an ecocyc GAF with ecocyc gene IDs as primary (analogous to dictybase etc).
Promotion of relations in Ensembl EBI pipeline
- consider a GO rule to "upgrade" acts-upstreamX relations to involved_in if separate IBA evidence
Update on NDex
- created a GO group on NDex
- will have a zoom call with Dexter and Jing to figure best way to produce cx files so they are indexed for IQuery (https://www.ndexbio.org/iquery/)