Manager Call 2019-04-24: Difference between revisions

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==Discussion points==
==Discussion points==
* Release : happened on March 19th; not yet released on April 17 - are there issues we should be addressing ?  
* Release : happened on March 19th; not yet released on April 17 - 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?


===Next hackathon===
===Next hackathon===

Revision as of 16:02, 22 April 2019

Agenda

  • 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; not yet released on April 17 - 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?

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 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.

Priorities until next GOC meeting

  • GO rules: priority - do we have resources now ?
    • Alex would like to know how rules also apply to other resources such as Protein2GO


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: 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 this spring to focus on the GPAD outputs generated from GO-CAM models?


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

New IEAs (not InterPro2GO)

https://github.com/geneontology/helpdesk/issues/195

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 ?

GPAD/GPI Specs

  • 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.

Minutes

Present