Manager Call 2020-09-30

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


Review GO meeting agenda

Any topics should be added ?

Project updates

Blocking issues/delays/changes in project scope

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

Review outstanding action items

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

  • 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

Projects updates

2020 Priorities:

Creating a static page for SPARQL endpoint

Mentioned in the NAR paper - this needs to be prioritized and resourced:

Legacy data (#6)

Update Laurent-Philippe


  • 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 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 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. Sp

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.

  • 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)