Manager Call 2020-09-23

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  • Present:
  • Regrets: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Judy, Paul, Laurent-Philippe,
  • Managers: Chris, David, Huaiyu, Laurent-Philippe, Kimberly, Pascale, Seth, Suzi, Judy, Paul


Agenda

Announcement

  • Pascale will be making the agenda for those calls from now on.
  • The main purpose of the calls is to report to PIs on projects progress, expected deliverables and delivery dates, delays, changes in project scope (unexpected tasks that need to be resourced).
  • Projects are based on the current projects, chosen and prioritized at/around each GO meeting - https://docs.google.com/document/d/1URLkEQBewlzD-NVAjbPLWD5Gu-5xq0RysTrm1GMbuiM/edit#
  • 2020 is a little different with the grant due in Jan 2021 - the deliverables will go to the end of 2020/early 2021 WRT what we want to show in the grant/preliminary data we need to produce
  • Everyone is of course invited to contribute discussion topics - add directly or ask Pascale. Pascale will be reviewing the agenda before calls
  • Everyone is of course invited to edit/fix minutes or action items if something is not correct.

Blocking issues/delays/changes in project scope

Anyone has blocking issues/delays/changes in project scope they need to report to managers /PIs?

Projects updates

2020 Priorities: https://docs.google.com/document/d/1URLkEQBewlzD-NVAjbPLWD5Gu-5xq0RysTrm1GMbuiM/edit#


GAF 2.2 (#4h) and GPAD/GPI 2.0 (#4i) (Kimberly)

  • Review action items

Draft the announcement and provide a link to the test file: https://docs.google.com/document/d/1x-jyBQgb4MoCdtNwxftbHJueP0n43Uz0PC_bZkH8ajw/edit

  • where to announce ? go-friends, go-announcements, GO website, biostars and other forums (R forum, others ?)?, fb, twitter, etc... etc
  • Mention we'll provide a GAF 2.2 -> 2.1 converter
  • What if some upstreams are not ready by Dec ? Will we add a default relation ?
    • Pascale proposes to keep the work easy for GO Central, and add the most general relation for any annotation for which the upstream did not provide anything. -> OK we agree (relations to be confirmed by Kimberly):
      • MF: enables
      • BP: acts upstream of or within
      • CC anatomical structure: located in
      • CC protein-containing complexes: part of
    • What about Protein2GO sources ? AgBase, PINC, etc ? Do we want to evaluate those individually and set the relation ?
  • Goal: December for consortium and March release for external users: can we re-consider January ? (this is mostly a technical question for Seth)
  • Helping converting annotations to more precise qualifier with PAINT, pathways and other strategies: without this information, for some species the new relation will not be very informative. Should we prioritize work to identify annotations that can use a more precise relation ?


  • Action Item Seth: Create a rule to repair the annotations that would be submitted as GAF2.1
  • Action Item Seth: Mention we'll provide a GAF 2.2 -> 2.1 converter & provide the converter
  • Action Item Seth: Look at OWL tools to see if they can handle extra relations
  • Action Item Laurent-Philippe: Check that there would be no impact on the API
  • Action Item Kimberly: Create example GAF2.2 (~10 lines) - cover all examples/combinations of qualifiers and relations

Noctua Imports (#3a)

Action items: Kimberly and David:

  • finalize annotation properties specs GPAD2.0 (metadata/history)
  • produce examples of issues with GPAD output
  • draft an agenda for a working meeting (~2days) to defines the requirements for GPAD output
  • priorities those issues to have different milestones and a better vision on when we could work with those ? (eg when for a 80% or 90% solution)

Next steps:

  1.  New MGI/WB files to be QC'ed (David & Kimberly)
  2. Finalize history/annotation properties GPAD2.0 specs
  3. Spec out GPAD output from GO-CAM models

Legacy data (#6)

Update Laurent-Philippe https://geneontology-test.s3.amazonaws.com/index.html

Deliverables

  • Ontology and annotations for as many prior releases as possible, available in /releases and on the GO archive in zenodo
    • GO archive: 2002-2011 (CVS) ; 2011-2018 (SVN)
      • OBO files: gene_ontology.obo (1.0 start 2004-02), gene_ontology_ext.obo = current go.obo (start 2009-03) ; discard gene_ontology-edit, gene_ontology-write, gene_ontology-1.2.obo
      • Slims: obo slims from mid 2004, discard "archived slims" which started in 2003
      • Adding all mysql dumps from archive.geneontology.org in mysql_dumps/
    • Note: a lot of jcvi GAFs from 2004-04 to 2011-03 (CVS) ; SVN: 2011-04 = single file to now; release.geneontology: 2018 to 2019-11 (not present after)
  • For these prior releases, up to when current release started, simple ontology files, and annotation files for top organisms (12 “reference genome” species) available for easy download from GO website (has not been prioritized yet)

Noctua (#3e)

  • ui implementations
    • bug fixes
      • Ongoing; Tremayne is submitting some PRs to noctua-dev for testing
      • Adding: connect to existing nodes; re-use of fields in a given model
    • ART
      • Tremayne has a prototype that David and Kimberly can test. The prototype has much of the desired functionality but is not yet employing the necessary functionality from minerva which will be developed later when Ben is available to work on that.

https://github.com/geneontology/noctua-annotation-review/issues/21

  • testing and release framework

Minerva support for noctua


Pipeline (ongoing) (#4)

  • 4a. Dustin is primary point of contact for pipeline failures, by December (Seth)

-> how is this going ?

  • 4b. Analysis of failure points in the pipeline and a plan to address them
  • 4c. Detection of large changes from last release, to find upstream issues earlier (Laurent-Philippe) snapshot -> prioritize ?

4d. Drop uniprot_noiea, add GO-reference-species


Pathways2GO paper (#1bi)

AOB

Creating a static page for SPARQL endpoint

Mentioned in the NAR paper - this needs to be prioritized and resourced: https://github.com/geneontology/go-site/issues/1549