Manager Call 2019-03-13

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Agenda

  • Agenda: Huaiyu
  • Minutes: Suzi

Management

  • Update on all ongoing projects: https://github.com/orgs/geneontology/projects -
    • Is anyone encountering any roadblocks?
  • We need % effort from the different people involved in project for all projects with a delivery date/active projects
  • 'Gantt-chart' to manage projects: Hackathon tasks: how is that working ?

Cambridge GOC Agenda

https://docs.google.com/document/d/1QiqfZ5eAwmljqt5Fh0Ooi1Pd-HKgMSGsYC_wx6-UEPY/edit


Discussion points

Implementation of taxon constraints

We'd like annotations failing taxon constraints to be excluded from AmiGO and all the files we export. Can we prioritize this task ? https://github.com/geneontology/go-ontology/issues/17025

'Redundant' PAINT annotations

  • Helen Atrill (and possibly others) would like to avoid making PAINT annotations from the same protein - ie would like to filter out GENE1 IBA with GENE1.
  • We had mentioned a while ago that there are 2 reasons to keep those:

1. Gives 'support' to the annotation in that it has been selected for PAINTing 2. (related to 1): could allow to display 'main' functions for each gene more prominently.

Do we want to implement anything relevant to that? If not, we might as well filter out these 'circular' annotations, which are certainly confusing for users.


Carried over form last week:

Fate of "unmanaged" external2go files

https://github.com/geneontology/go-ontology/issues/16989

New IEAs (not InterPro2GO)

https://github.com/geneontology/helpdesk/issues/195

We decided earlier to not accept IEAs from outside groups, as all sequences would be run through the dependable InterPro2GO after uploading- but this group/method *seems* like they have more accurate annotations and higher coverage.

SynGO import

Long discussion last week - What's the next step ?

GPAD/GPI Specs

  • We were going to set up a call - has it be scheduled?
    • Chris was going to review current specs, particularly wrt SO/MSO
  • Discuss expanding the gpi file to include other entities used in annotation, particularly the With/From field. e.g. variation IDs, RNAi experiment IDs, etc.
    • This has come up in discussions with several curation groups, including MGI, WB, and Zfin
    • How does the GO gpi file work fit in with Alliance data files?
    • Not all GO contributors are part of the Alliance, but it would be nice to have standardized file formats for other entities.

New topics

BioLink availability: plan to durably solve those issues (last week we had timeout, this morning internal server error) ? Reference: https://agr-jira.atlassian.net/browse/AGR-1454

Minutes

Present