Manager Call 2020-11-11

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


Agenda

Announcement

GO-CAM jamboree next week: no managers call

Follow up on ACTION ITEMS

  • 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 (https://royalsocietypublishing.org/doi/10.1098/rsob.180241) https://www.pombase.org/browse-curation/fission-yeast-go-slimming-tips -> Suzi to write up documentation based on SGD doc
  • AI: Rhea2GO mappings: Pascale to contact Alex with help if needed from Alan, Jim, Anne, Harold, Peter, others DONE in progress
  • syngo: uniprot and MOD harmonization
    • 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.
    • Paul talked with SynGO - Issue was with isoforms mapped on TrEMBL. Dustin is checking whether all entries can be mapped / get a report on which ones cannot be mapped
  • more regular meeting breaks -> more precise proposal ?

GO-CAM jamboree next week

- Any specific needs ? - Goals

New member BBOP

Seth: BBOP, for various projects, is experimenting with some LBL in-house contracting. As a pilot project, we're having him work on some of the dockerization/devops stuff for the GO, which is on the critical path for Imports, etc., so nice. I didn't want you confused if Chris or myself mention Abdel in conversation. He may also turn up on the software list or calls in the future, depending on how things proceed.

Announce that the SVN is dead

Kim from Pombase was still using SVN to get the xrefs - https://github.com/geneontology/go-site/issues/1570 We need to communicate better- annotation calls and GO meetings are not enough.

  • How about we announce it on the GO-announcement repo and go-friends, and maybe tweet/facebook the 'new' download/legacy download addresses ?
  • ACTION ITEM Suzi send to go-friends and other lists
  • ACTION ITEM Suzi/Pascale identify people that should sign up

Release status

Pascale approved > 1 week ago -> status ?

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?


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)

  • We will need to dedicate more resources to getting GAF 2.2 out the door (smoothly). Who should this be? Kimberly, Pascale, Seth, Eric???

https://github.com/geneontology/go-site/issues/1558

  • 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

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

  • Laurent-Philippe says he's not sure it works for programmatic access, needs to be checked
  • Chris says it's important to do this since we mention it in the paper
  • Need to make the static landing page

Legacy data (#6)

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

Migration of WormBase and MGI to Noctua(#3a)

GO reference species

Data set is twice as large as what we currently load, which slows down the pipeline significantly Will look into optimization


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.

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

  • testing and release framework