Manager Call 2020-10-28

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


Follow up on ACTION ITEMS/Future breakouts/projects

  • AI ncRNA annotations, id space, etc. Suggestion is to involve RNAcentral in this. RNAcentral has their consortium meeting on Nov. 20th
    • contact RNAcentral (Anton Petrov): Pascale/Paul
      • to understand/document their process and see whether we should attend the consortium meeting
  • AI: Point users to slim generating tools and provide an SOP ( -> Suzi to write up documentation based on SGD doc
      • Suzi to create a ticket
  • Retrofitting gp2term relations: Kimberly: this is pretty urgent, should be done before the next grant: Kimberly/David to propose deliverables and try to estimate resources so we can prioritize this
  • AI: Deadline for GAF2.2: Curtis Ross : Kimberly to generate test files & send the announcement to go-friends and go-announcement repo and biostars and others (also need to have a 2.2 -> 2.1 converter)
  • AI: Rhea2GO mappings: Pascale to contact Alex with help if needed from Alan, Jim, Anne, Harold, Peter, others
  • GO-CAM guidelines and functionality:
    • stoichiometry assertions in GO-CAM'(interested: Darren Natale;...)
    • Annotation of ncRNAs - Ruth
    • cell type specificity - Ruth
    • annotating proteoforms/ or rather protein chains (viruses but also some non-viral proteins) (interested: Darren Natale;...)
  • Annotation review process: current one is clumsy and hard to do stats with -> Pascale to add this to GO grant ideas - DONE
  • AI: Student Curation/Teaching GO annotations / community curation: use of students for curating, educational value, does it actually save curator time or not, students cross-checking each other. Model after successful CACAO project. Something to possibly explore for the next grant. Pascale to add this to GO grant ideas - DONE

Other topics

  • syngo: uniprot and MOD harmonization
  • more regular meeting breaks

- Problem is that there is more than 1 ID space for a species due to SynGO annotating UniProt entries for MODs. We need to map to MOD IDs to make it consistent with other data.

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)

  • Urgent: we need to indicate what relations to use with asserted root annotations to BP and CC.
    • DECISION: Most consistent with our data model is that all genes enables some MF and all MF are part of some BP => involved_in and CC 0> is active in
  • 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
    • Not expected to be an issue, we'll see when we load in snapshot
  • Action Item Laurent-Philippe: Check that there would be no impact on the API
    • Needs to be checked
  • 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)