Manager Call 2020-02-12

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  • Agenda: Suzi
  • Minutes: Seth
  • Present: Suzi, Seth, Judy, Pascale, Huaiyu, Chris, Laurent, Paul, Kimberly
  • Regrets: "To regret deeply is to live afresh" -- Henry David Thoreau

Discussion points

Upcoming Meetings

Caltech f2f, 24-28 Feb

GO meeting Paris, 11 (Users), 12-14 (Main), 15(SAB) May

GO meeting Baltimore, week of 5th Oct


Release delays

Is there anything we can do to help make releases easier ?

Status of 'high priority' Projects

Google spreadsheet of the projects:

  • We need to know which of those projects are being worked on.
  • Also, are there other projects not in this list ? to be sure the priorities are aligned with the specification documents and vice versa.

AmiGO search fixes

Not yet prioritized but the PIs asked to evaluate work to decide whether this will be prioritized Seth/Chris: evaluation of time - prioritization - resources

2.2 Aggregate Statistics for releases

2.3 Legacy infrastructure

3.1 Migration of MGI and WormBase annotations to Noctua

Week of Feb 24 hackaton will address that: Aims meeting:

  • The primary product of this meeting will be a gantt chart (see David’s from MGI’s perspective) that fully describes input and output switchover dependencies at the three sites (although not necessarily times, as some of this will be dictated by other resource limitations). The document will define future work on this project.
  • A secondary product will be to have a plan for annotation history. (TASK 4.5 in Priorities doc)
  • A secondary product will be to have a base validation format that is usable for both batch rules and minerva UI signals. (TASK #?? Priority? )
  • A secondary product will be continued work on merging the GPAD codebase and RDF emitters into the ontobio library. (TASK #?? Priority? )

4.1 GO-CAM ShEx specification v1.0 completion

4.2 Integrating validation (AKA GO rules) into Minerva

4.3 Noctua/GO-CAM Curator Documentation: curation philosophy

4.4: Documentation: curation how-to

  • which relations to choose when - this is the main thing curators ask about

-> Kimberly in progress

4.8 Pathways2GO, including making models *activity-centric*

5.1 Deploy Noctua Search (as landing page)

5.3 Noctua onto "production" footing

8.7 Improve GO API & support the GO-CAM + documentation

Other discussion points

Loading viral and bacterial entries in NEO Prioritize + assign someone

Isoforms not loaded in AmiGO

Was there a decision NOT to include UniProt isoforms in AmiGO ?

Also - should we provide single files for each organism, rather than splitting by entity type ?


  • Caltech f2f:
    Seth/Kimberly: all good
  • Paris GO meeting:
    LP: still waiting for feedback, in delay; hopefully response this week; will add recommendations to the wiki; no block reserved
  • AmiGO search fixes:
    Seth: I’m blocking this for the moment
  • 2.2 Aggregate stats:
    LP: Starting again
    Chris: what is this?
    Pascale: some fixes; add pubmed; go-cam stats
    LP: discussion about go-cam metrics, today?
    Chris: are prioritizing right?
    LP: independent, no need right now
    LP: legacy can start soon.
    Chris: finish aggregate stats quickly; about how much time?
    LP: two/three days
    Chris: then amigo search fixes?
    LP: other priorities too
  • 2.3 Legacy infrastructure:
    Seth: Happening soon, hopefully. Will chat on Thursday.
  • Caltech data flow agenda:
    Pascale: A little confused by format of hackathon doc, will talk to Seth later
  • 4.1 GO-CAM ShEx specification v1.0 completion
    Kimberly: last into shex, more could be put in; will talk about the work that ben has done closing the shapes; next thing for dustin to use shex to validate imports;
    Pascale: almost finished?
    Kimberly: almost there
  • 4.2 Integrating validation (AKA GO rules) into Minerva
    Pascale: will check with ben; define a whole project document
  • Noctua form:
    Judy: a lot of tickets
    Kimberly: these are being worked on
  • 4.3 Noctua/GO-CAM Curator Documentation: curation philosophy
    Pascale: curator docs finished?
    Kimberly: basics done, needs polish and some more work
  • 4.8 Pathways2GO, including making models *activity-centric*
    Judy: working with…?
    Kimberly: a few small things to tidy up with respect to modeling decisions;
    Seth: react now in
    Chris: this phase is go-cams coming from reactome; next phase will be making the more go-cam-like
    Kimberly: final aspect is gpad outputs
  • 5.1 Deploy Noctua Search (as landing page)
    Kimberly: spec doc, impl doc, go over those today;
    LP: will send doc to chris later
  • 5.3 Noctua onto "production" footing
    Seth: devops; this is not a new thing; definition of devops
  • 8.7 Improve GO API & support the GO-CAM + documentation
    Chris: we decided to go ahead with core GO API and robustifying it, but not supporting GO-CAM in APIs at this stage;
  • Isoforms:
    Chris: thinks it’s the GCRP issue, the reason we split it out. Seems to want to look into it.
    Pascale: If tell alan to exclude, should be able to load
    Chris: They should just have one file
    Pascale: will ask alex
  • NEO load addition: get a URL for the uniprot bacteria; Seth to look at file
  • Releases:
    Pascale: Can we improve releases: Seth will ponder
  • Future work:
    Chris: can we start working on ontology releases again;
    Pascale: working with Val
    Kimberly: for next round of funding, think about annotation priorities;
    Judy: beyond GO-CAM; what resources do we have and how do we prioritize?
    Kimberly: we’ve tried to work on different areas of biology (e.g. signalling pathways); still there is a tension about what go puts out vs/ the MODs; for the next round, let’s be clear about how we want to spend our annotation resources.