Manager Call 2020-04-22

Agenda

• Agenda: Laurent-Philippe
• Minutes: David
• Present:
• Regrets:

May Consortium Meetings

Notes from meeting are in bold

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

ACTION: Finalize and discuss on next week's managers call

Genes - Invitation to edit special issue on Gene Ontology

• Paola was invited to be a guest editor for a special issue on GO for the open-access journal Genes
• She forwarded the email to Chris, David, Kimberly, and Pascale
• Is this a good opportunity to communicate some of the recent changes to GO?
• How much work would this be and for whom?

• "We invite you to join us as Guest Editor for the open access journal Genes (ISSN 2073-4425), to establish a Special Issue. Our suggested topic is ‘Gene Ontology’. [edits] As Guest Editor, we would ask you to define the aim and scope of the Special Issue, assist in inviting contributions, be the final decision-maker for articles after peer-review, and collaborate with our editorial team at MDPI. [edit] The editorial office will take care of setting up the Special Issue website, arranging for promotional material, assisting with invitations to contribute papers, and administrative tasks associated with peer-review, including inviting reviewers, collating reports, contacting authors, and professional production before publication."

GAF2.2

DECISIONS:

• Time line: 4 months?
• Actions:

1. Pascale/Seth: Write formal specs documentation - ONGOING - some small fixes needed
2. Kimberly, David, Laurent-Phlippe: Write usage notes: aim in 2 weeks: Draft of announcement and usage notes - ONGOING - feedback invited
3. 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
4. Send notice
5. Eric/Seth Adjust scripts
6. Paul's group: Adjust enrichment tools

XenBase onboarding

ACTIONS

• 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

Seth: no news from Malcom. Will follow up.

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

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

• https://github.com/evidenceontology/evidenceontology/issues/251

• Many Evidence codes do not match to the 3-letter evidence codes that we would map to
• ACTION: Pascale to contact Michelle to set up some virtual meeting to discuss some issues we'd like to see fixed

Expertise - biological and/or technical and users.yaml versus group-contacts.tsv

https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv https://github.com/geneontology/go-site/blob/master/metadata/users.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 handles
• group-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 ?

• Judy, Paul, Kimberly: would be nice to have expertise file
• Paul: would like to use a GO term - high level term if possible
• Maybe an activity for the GO virtual meeting

Publications

• Val's matrix paper is available as a draft
• Sent to go-top
• Not on biorxiv as of 2020-04-21