Manager Call 2019-05-15

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Agenda

  • Agenda: Seth
  • Minutes: Pascale

GO annotation in Apollo

Kimberly

  • EuPathDB is interested in using Apollo for functional annotation
  • How does this fit into our overall plan for developing tools for GO curation and working with new groups?

Discussion

    • To be discussed when Chris and Seth are present (next week?)

Priorities until next GOC meeting

Everyone was to fill in their effort (number of days until the GO meeting) for each Priority 1 project.

Items carried over from previous meetings

NOTE: Some of them may be resolved - ALL: please check and add decision as appropriate.


AGR & GO widgets

The proposal to create GO term pages on the AGR site has come up again during the Biological Function call. If AGR creates GO term pages, the data could be fetched either from GO or from the AGR database. Data consistency & "correctness" could become a problem if choosing the later as the AGR integration process of GO is different.

Laurent-Philippe has asked for a UI mockup to better understand the AGR requirements and how the current amigo pages does not currently meet them. What is the GO consortium position on that matter ? (new GO term pages vs improving / redoing amigo; fetching the data from GO or from the AGR database for those pages) Discussion

  • We (GO) will create the page that will be in AGR, and make it using reusable web components so that we can use it in AmiGO as well.

Helpdesk

  • Seth was to talk to Todd Harris to see how WormBase has implemented their helpdesk system
    • Recently contacted Todd, no concrete progress/results -Seth
    • Judy suggests to contact David Shaw at MGI

Discussion

Authoritative groups

Managers: do we need to change the policy ? For example SynGO annotated mouse and rat; MGI submits the SynGO annotations but not RGD (and anyway GOC would prefer to do the integration itself).

Discussion

    • Judy: we should contact RGD (Pascale: and all other impacted resources) and ask them whether they would be willing to have the SynGO data loaded directly
    • Paul: Paul S mentioned that he (wormbase) would be OK to just be able to review the data (in Noctua); the data flow doesn't need to go through wormbase
    • Proposed process:
      • SynGO data would be loaded directly into the GO database
      • SynGO data would be filtered out from the MOD/contributors files (like PAINT)
      • Authoritative databases would keep control of the annotations; they could review/give feedback (?)/edit annotations
    • Actions
      • Check whether doable (Seth?)
      • MGI and other groups stop loading SynGO annotations directly - would load by the GO pipeline
      • Paul T to contact SynGO and all impacted groups to explain the proposed process:

Releases

  • Can we produce human-readable (Error) reports if something goes wrong with the pipeline - for example missing files (for example right now uniprot-all is missing)
  • Annotation and Ontology stats: it would be nice to track changes in the ontology and annotations by looking at the differences between releases. Can resources be assigned to this ? See also https://s3.amazonaws.com/geneontology-public/go-stats.tsv and https://s3.amazonaws.com/geneontology-public/go-last-changes.tsv (Laurent-Philippe) (info about which terms have been obsoleted, which are the new terms, etc).
  • The QC group can provide specs if there are resources to implement it.

Meeting with MOD developers to go over GO pipeline

BioLink availability [SOLVED]

Plan to durably solve those issues (last week we had timeout, this morning internal server error) ?

    • Reference: https://agr-jira.atlassian.net/browse/AGR-1454
    • Current strategy: server api.geneontology.org up and running for more than 2 weeks. Health checks every 30s, if fails, sends sms + email notification + auto relaunch the server after 1m30. BioLink timeouts of 4s are increased to 15s as it was causing issues and the id conversion is now handled by mygene (Deepak fix). GOLr would gain to have a docker or VM that could also auto relaunch in case of failures and scale on demand.

Pipeline

  • We need an SOP for how to handle annotation (or other?) files that have pipeline-blocking errors that can be fixed by GO
    • Is it okay to fix these errors?
    • If yes, then is it okay to point to a GO version of the file in the source URL in the datasets.yaml file until the source file is fixed?

GO-CAM models GPAD outputs

  • Should Kimberly and David plan to go to visit Jim some time in August to focus on the GPAD outputs generated from GO-CAM models? Could also work on:
    • Annotation extensions
    • removing regulates_o_part of chain
    • Spatial relations
    • chemicals at pH7.3

Fate of "unmanaged" external2go files

https://github.com/geneontology/go-ontology/issues/16989

  • Ontology group would like to archived them since we don't have the resources to maintain them and no one is maintaining these (e.g. mips is deprecated).

Must list which projects are not maintained anymore, and at least simplify the list. Waiting from Paul review. It seems tigr will be maintained by NCBI.

external2go svn link: http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/external2go/

Also looking at "Genome Properties" for GO mappings. Chris will put some slides on this for microbial annotations, possibly another grant to have sufficient resources.

Note that there has been a discussion of why the Reactome file hasn't been updated. https://github.com/geneontology/go-site/issues/1031

Minutes

Present: Pascale, Huaiyu, Laurent-Philippe, Kimberly, Paul, David, Judy, Suzi