Manager Call 2019-05-01

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Agenda

  • Agenda: David
  • Minutes: Suzi


Next priority: Distinguishing between Causal Activity Models and Standard Annotations (SA)

Following up on last week's call. From the last GO-CAM call (April 23rd), it's clear that curators need more guidance as to what is a GO-CAM model and what is expected from them to produce a GO-CAM. As well, Noctua allows to do both curation of GO-CAMs and to do standard annotations (and annotation sets). This needs to be clarified, as some curators think they should be using Noctua only to curate GO-CAMs. We want to let people know they can do both.

Next steps:

  1. Glossary: Move to wiki? https://docs.google.com/document/d/1w3mkF1RQIzwROOCMTkqjYaOn8ZbdsW52t-xA4DKt0vg/edit?ts=5cc0ffef#
  2. Define 'Causal Activity Model': Proposal: A CAM contains at least one causal relation between two functions (regulates, causally upstream of, etc - WHAT IS MISSING?) (maybe add as a note: a GO-CAM should havemore information than what we can add to an annotation extension)
  3. Use this definition of a GO-CAM to automatically classify models as GO-Causal Activity Models or Standard Annotation
  4. In Noctua/workbenches: Develop some display to indicate GO-CAM vs SA (logo?)
  5. For users: Change the GO-CAM display page to only show GO-CAMs (SA would only be shown in AmiGO)

June face to face meeting

Pascale and Kimberly will be in LA in June - we could take advantage of this to hold a meeting. Possibly June 17th-20th

  • Won't work for David. This is curator week in Bar Harbor.

GO meeting Action items

Each group should have reviewed their action items, create GH tickets as necessary and bring any outstanding issue back to the managers call:

AGR & GO term pages

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)

Priorities until next GOC meeting

Following up on discussion points form last week

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

GO-CAM vs annotation

  • Kimberly: documentation

Discussion points

Discussion points carried over from previous meetings

  • 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.


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?
    • Annotation extensions
    • removing regulates_o_partof 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

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 been 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

Next priority: Distinguishing between Causal Activity Models and Standard Annotations (SA):

KVA: Version of SA documentation should live on wiki. Should we have a cam vs. standard (sa) status on Noctua, export SA as-is but CAMs displayed on website.

CM: Automatic decision?

KVA: not decided

PT: SAs are the simplest CAMs, is this distinction necessary? Noctua is a general annotation tool, this isn't a conceptual leap from current practice. Would rather explain this difference than change.

KVA: Need to make curators more comfortable with making sets of SAs, and if these are causal models

PT: Distinction may not be necessary- now with more expressive framework, but not necessary to make it. Advanced tooling, but don't have to make it.

JB: Can already make a SA with just one click, this is a training issue

CM: Discussion may be red herring, problem is getting curators on board

PT: Repository is the way to store- SAs is one export, network pathways is another, etc. CAM is framework, available but missing in most cases still. Conversion is in progress.

KVA: This conversation came from last week's annotation call, about naming- then turned into "what is a model".

CM: Display issue- display should make this more clear. Users don't yet understand how they'll interact with these annotations.

JB: Usable & interpretable by general public- this is important but not yet in place for GO

PT: Key product now is into historical product- what users always have gotten from GO. Will be a lag before vision becomes reality.

KVA: Curators need to have vision articulated more clearly- timeline, current expectations. Be very clear about what average curator should be able to do at this moment.

Pascale: Exports not working currently (extensions).

PT: MODs seem to be only ones using extensions.

KVA: Put together a document of what current/future standards/abilities curators should have.


  • Managers should work on the message to curators before this is next on GO-CAM/GO Annotation calls.

PT: Users will progress (perhaps slowly) as they use Noctua more & more.

JB: This is a general annotation switch-over, interconnectivity and old habits will play into migration

SC: Rebranding, ART (annotation review tool) is coming out, this may be a good time to rename/name/presenting things in a unified manner.

SA: Extensions in simple annotations are stopping some groups- defined documentation is needed in this new push.

CM: Simple causal relations are necessary in some of these, not being used/curators not aware of this. GO-CAM Usage working group?

JB: Utility & power of model needs to be demonstrated.

CM: Need to work closely with outside groups that will use these models.


F2F:

in LA in June(?)

CM has tentative commitment for 18th-ish of June


  • Need to determine why we're meeting, then can determine when/who

AGR & GO term pages:

CM: Will be a GO page in AGR, mockup will be Amigoesque with some feature requests. Reuse same code in future versions of AmiGO (??).

PT: Shared infrastructure supports AGR. Consistency with ribbon.

CM: Need this to be extensable, showing causual relations, etc.

JB: Higher traffic expected for AGR, this will be beneficial for GO.

KVA: Purpose is to preserve look & feel of ARG ontology pages for GO data.


Helpdesk:

SC: No word back from WB,

JB: Possibly talk to David Shaw about MGI's methods.


  • Need standard name for go.org/GO-CAM site: GO-Cam Portal (?)

Present

Chris, David, Judy, Kimberly, Laurent-Philippe, Paul, Seth, Suzi