Manager Call 2020-04-15
- 1 Agenda
- 1.1 May Consortium Meetings
- 1.2 Update on actions from last call
- 1.3 Discussion topics
- 1.4 Topics not discussed on last call
- Agenda: Pascale
- Minutes: Laurent-Philippe
May Consortium Meetings
- We are within a month of the May consortium meetings
- Need to start firming up the agenda so people can start planning their schedules and working on presentations
Update on actions from last call
- Time line: 4 months?
- Pascale/Seth: Write formal specs documentation
- Kimberly, David, Laurent-Phlippe: Write usage notes: aim in 2 weeks: Draft of announcement and usage notes
- Kimberly, David, Laurent-Phlippe: Write some FAQs: what is the impact; why are we doing this ? Clarify the way a gene is related to a GO term
- Send notice
- Eric/Seth Adjust scripts
- Paul's group: Adjust enrichment tools
- Seth will ask Malcom for his files, this will allow to test his pipeline
- Kimberly and David will continue training XenBase curators, they will join the call
- Jim is adding the Xenopus anatomy to the imports
Topics not discussed on last call
GO grant highlights and vision
Google doc with abridged grant with vision sections highlighted: https://docs.google.com/document/d/1t_Ube-ngprwBhyoKh5lDgtYYoQztl3yV1ETcfxrpquk
Collect current issues (eg genes that can not be found) to start improving it
Component for GO annotations in journals
Considering 1) easy to integrate web component and 2) current covid situation where submerged by literature difficult to mine retrospectively, try again to propose a very lightweight tool, probably optional, but that would allow an author to provide (gene, function) associations while submitting. Best journals to try ? biorxiv ?
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
See discussion in https://github.com/geneontology/go-site/pull/1447
userscontain all users, including people not on the project anymore
- Not sure where affiliations come from for eg Cath Brooksbank listed as GO_central).
usersdoes not have GH handles
group-contactsincludes 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 ?
- 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?