Manager Call 2020-04-22

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Agenda

  • Agenda: David
  • Minutes: Kimberly
  • Present: David, Judy, Kimberly, Pascale, Seth, Suzi
  • Regrets:

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: Updated meeting agenda - please review

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."

ACTION: Pascale will forward email to go-directors with recommendation from managers that we not pursue this right now.

Transcription workshop next week

  • Ruth, Pascale
  • Was supposed to be at EBI next week. Will hold remotely.

GAF2.2

DECISIONS:

  • Time line: 4 months? We need a more defined timeline here. Seth will create a github project for planning purposes.
  • 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.

ACTION ITEM: Consider starting a working group to discuss external ontologies in Noctua and GO more generally with the goal of developing consistent representation (as much as possible) and an SOP to give to groups onboarding. Will discuss further on the GO-CAM specs call, particularly with Jim B.

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

  • 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
    • -> PascaleEmailed 2020-04-29

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

Need to decide the best place to keep the expertise information, knowing that people come and go in the project.

Publications

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