Manager Call 2019-04-24

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  • Agenda: Kimberly
  • Minutes: Huaiyu

Calls after the GO meeting

  • We propose to cancel all GO calls the week after the GO meeting
  • Also, if there are 5 weeks in a month, we could also cancel calls on that last week

GO meeting recap

Discussion points

  • Release : happened on March 19th; and April 18 - are there issues we should be addressing ?
  • noctua-dev is being used for testing imports, but it is often really slow for loading or editing/creating models. Is there anything that can be done to improve the performance?
    • Once all of WB and MGI models are loaded onto noctua, will we have the same issue?
  • GO-CAM versus an annotation: we need to clarify what GO-CAMs are: (connection of at least 2 activities), versus lists of annotations (like the XenBase phenotypes, for example). We need to allow both usecases.
    • One possible way to deal with this is to have MODs annotate 'normal' annotations, and GO Central have curators doing models (based on MOD annotations if appropriate)

Seth and Dustin trip to BHB


Next hackathon

Chris, Paul

Discussion points from GOC meeting

  • Helpdesk email: Seth + Managers: work out a long term solution for the helpdesk
  • 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).
  • 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 and (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.

Priorities until next GOC meeting

Discussion points carried over from previous meetings

Meeting with MOD developers to go over GO pipeline

BioLink availability

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

    • Reference:
    • Current strategy: server 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.


  • 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 this spring to focus on the GPAD outputs generated from GO-CAM models?
    • Annotation extensions
    • removing regulates_o_partof chain
    • Spatial relations
    • chemicals at pH7.3

Fate of "unmanaged" external2go files

  • 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:

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.

New IEAs (not InterPro2GO)

We decided earlier to not accept IEAs from outside groups, as all sequences would be run through the dependable InterPro2GO after uploading- but this group/method *seems* like they have more accurate annotations and higher coverage.

SynGO import

Long discussion last week - What's the next step ?


  • We were going to set up a call - has it be scheduled?
    • Chris was going to review current specs, particularly wrt SO/MSO
  • Discuss expanding the gpi file to include other entities used in annotation, particularly the With/From field. e.g. variation IDs, RNAi experiment IDs, etc.
    • This has come up in discussions with several curation groups, including MGI, WB, and Zfin
    • How does the GO gpi file work fit in with Alliance data files?
    • Not all GO contributors are part of the Alliance, but it would be nice to have standardized file formats for other entities.



Judy, Pascale, Huaiyu, Suzi, Kimberly, David, Chris, Seth

GO Conference Calls

  • Only the calls in the week after the GOC meeting will be canceled.
  • Applies to all the GO calls, but not alliance calls.
  • This will be announced at the October GO meeting. Suzi will put a note in the agenda.

GO meeting recap

  • There is a google doc with action items compiled by Pascale. See the link above.
  • They are assigned to individuals.
  • Will discuss with each group. Some discussing points are in the agenda for this call.


  • David: The March release was delayed by MGI.
  • Seth: Probably needs more resources to fix issues
  • Chris asked whether it is possible to add Dustin to help on the release pipeline. Huaiyu explained that Dustin is currently working on three parallel projects, and it would be helpful to know exactly the tasks (either long-term or short-term). Will continue the discussion offline.


  • Landing page is slow loading - Seth: this is a know issue.
  • Seth: If it is slow using the editing tool, it is an issue. Should report if this happens.
  • The slowness is in comparison with the production. Kimberly experienced the problem of taking a minute or so to add an evidence. Will report if this happens again, and Seth agrees to look into the problem.