Manager Call 2020-12-02

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


Agenda

Announcements

  • First 'GO call vacation week next week' -- no call Dec 9th

December Items

  • Alliance All Hands Meeting next week - any action(s) needed from GO managers/other personnel?
  • Progress Reports - who, when, what format?


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
      • Paul -> RNA Central is planning to create 'Reference RNomes' (not sure how they are called) - for which species ?
      • We can send RNA types or species we are interested in, they would prioritize this
      • Run proposal by Consortium: what do we need ? (a) reference species ? (b) species who annotate RNAs ? Paul : b.
      • AI: ask who annotates RNA and need RNA central to curate their genomes
  • 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; scalability issue
    • Rhea mappings create 20 million new annotations
    • This will keep getting worse - Tree of Life project will be adding 100s on thousands of species (200k?)
  • 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

GO-CAM jamboree recap/actions/priorities

Kimberly

  • People generally happy with the jamboree and we got good feedback about the tool
  • Sabrina and David gave feedback about time it takes to make models
  • Nice to sit down for a block of time to discuss specific issues, also for curators
  • After current 'sprint, will use feedback from users to prioritize next tasks, especially model copy, mentioned many times
  • David mentions the jamboree helped curate processes that had no annotations in MGI
  • Paul: noticed that people like the graph view, we need to have an intuitive, easy to use graphical view
  • Model copy: Paul and Chris spoke to Peter to see what he wanted as attribution for model copy; he was ok with *not* having Reactome (say) as a contributor for model copy on individual annotations, just some attribution/tracking that this is where the model is coming from
  • Pascale this model would be consistent with scientific citations
  • Kimberly proposes to spec it out and present on an annotation call also with examples
  • Kimberly would like the curator of the original model to be credited if there are only changes to the model, for eg cell type.
  • Seth: model proposed by Peter/Paul/Chris easy to implement; we can later implement model diffs if later we need more information
  • Laurent-Philippe: what happens if the original model changes ? Laurent-Philippe says we should have a tag from which model the model is derived; the original
  • AI: Kimberly and the Noctua WG to propose specifications once ART is done

Asynchrony between the ontology and the annotations

A few annotations made to terms that have been obsoleted late in the release cycle 'miss' the checks, so we often export annotations to terms that are obsoleted, even based on the version of the ontology we export

  • Do we want to increase priorities/resources on fixing this issue ?
  • There are other tasks we want to do first. Especially the rewritting of the kernel, otherwise we will need to write the fix twice
  • AI to make plan offline to 'freeze' obsoletions and merges until late in the release

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

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

  • DONE (added to documentation): 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 - IN PROGRESS: Create a rule to repair the annotations that would be submitted as GAF2.1
  • Action Item Seth - DONE: Mention in the announcement email we'll provide a GAF 2.2 -> 2.1 converter & provide a link to the converter
  • Action Item Seth (won't need to do until March): 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 - DONE?: Check that there would be no impact on the API
    • Needs to be checked after we implement new file
  • Action Item Kimberly - DONE: Create example GAF2.2 (~10 lines) - cover all examples/combinations of qualifiers and relations
  • Need to provide test files and links to other software resources (e.g. converter - see above) so we can send out the announcement email.
  • Action item Kimberly - TO DO: Contact individual groups to make sure they're all on track for GAF 2.2 (particularly groups that don't normally attend the annotation calls)

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