Manager Call 2020-04-08
Agenda
- Agenda: Seth
- Minutes: Pascale
- Present:
- Regrets:
Discussion points
GAF2.2 relations qualifiers
Kimberly and Pascale drafted specs: https://github.com/geneontology/go-annotation/issues/2917
- What's the next step ?
- Will we support both files to load from the MODs ?
- Will we produce both files, so people don't need to adjust parsers if they don't have the resources
MGI and WB Imports
Status updates
- WB
- Alex will work on preparing a test GPAD file with annotation history for WB - hopes to have it on the GOA ftp site soon
- MGI
- Have a periodic follow-up call to review progress?
- Sidenote: interest from XenBase, want to get Noctua annotations into AmiGO. Can we just fast track these through (directly load, not go back through XenBase)? No legacy history attached. https://github.com/geneontology/go-site/issues/1434.
Xenbase into GO main
- Malcolm already attends Judy's meeting, TO-DO: invite him (and/or xenbase reps) to GO-annotation calls. Need to make sure XB maintains own annotations, is in line with GO SOPs.
Pathway Genome Databases and the Alliance
See Chris' email
- Explore bringing in other existing curated pathways in a similar way that we did for Reactome
- Follow-up to Alliance call with Peter K. two weeks ago?
ECO and IEAs
In GPAD we mandate use of ECO over evidence codes. However, have we properly evaluated ECO for its use here? There is a massive mismatch in the GO meaning of IEA and the mapped term in ECO, see
Users versus group-contacts.yaml
https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv https://github.com/geneontology/go-site/blob/master/metadata/groups.yaml
See discussion in https://github.com/geneontology/go-site/pull/1447
users
contain all users, including people not on the project anymore- Not sure where affiliations come from for eg Cath Brooksbank listed as GO_central).
users
does not have GH handlesgroup-contacts
includes only active members- 'Expertise' should like people's expertise or role (developer/curator)
-> How do we want to use those two files moving forward ? Do we need two files ?
Publications
- Val's matrix paper is available as a draft
- Authors have reviewed and made comments
- Do the GO PIs (besides Chris who is last author) also need to read?