LEGO September 19, 2016

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Bluejeans URL - NOTE NEW MEETING TIME: 8:00am PST

https://bluejeans.com/969313231

Agenda

Training and Documentation

USC Training Session

  • It will be held 2016-11-07, the Monday after the consortium meeting
    • We will probably need to do another session as well. Zfin will probably want a session on site and the SGD curators may be able to piggyback on that session.

Documentation

  • Some comments and edits made to the Quick Start guide
  • Any more comments on Quick Start Guide?
    • The new quickstart page is linked from the web site now.
    • We should change the learn more button to something else. It is not clear exactly where it will lead. It could simply be an 'about the project' page. We need to make it clear that it is instructions.
  • We would like to make an FAQ.

Software Updates

Updates to UI

NEO Overview and GPI Files

  • Questions, issues still to be sorted out?
        • Chris will present his GPI talk at the GOC meeting.
    • We have entries for:
      • Genes
      • Proteins
      • Transcripts
      • ncRNAs
      • Protein Complexes
    • How should protein complexes be represented?
  • David will modify the wiki that describes the GPI specs.

GAF/GPAD Outputs

  • Set up time for meetings on this.

MGI Meeting Follow Up

  • Review the list of software and annotation issues that were discussed at the MGI training session, June 15th-16th.
  • See the Google doc
  • Some specific follow-up:
    • GAF/GPAD output is probably highest priority
      • Remaining issues:
        • How to handle causal chains
        • Multiple evidence = multiple lines in the GAF
    • We still need to figure out attribution. Right now everything coming in from Noctua has the group attribute GO_Noctua. That means that different groups making annotations to mouse genes cannot be distinguished.

LEGO Relations

  • New relations needed:
    • removes_input
      • directionality for causally_upstream_of_or_within and causally_upstream_of
        • GH tickets have been created to request these relations.

Minutes

  • On call: Barbara, Chris, David H., David OS, Jim, Kimberly, Midori, Sabrina, Seth, Stacia

Software Updates

Training and Documentation

USC Training Session

  • Will have a training session on Monday, November 7th.

GAF/GPAD Outputs

  • There is a github ticket for GAF/GPAD outputs.
  • Curators should put any questions about GAF/GPAD outputs from their models on this ticket.
  • Still pulling files from folder in Jenkins directory
  • Stable, final URL still needed; dependent on new pipeline
  • David H, David OS, Jim, Kimberly will set up time to resume GAF/GPAD calls to finalize these outputs
    • Doodle poll to find a good time for everyone

Documentation

  • QuickStart Guide
  • LEGO Google doc - longer, more philosophical discussion
  • FAQs - please suggest questions

NEO Overview and GPI Files

  • Frequency of NEO updates?
    • In theory, can go to an automated cycle for NEO updates, but would still like to do manual for now
    • Once the new pipeline is in place, daily updates, possibly even more frequently
    • Only takes a few hours to load
  • Plans to grab gpi files from different groups' ftp sites? (as opposed to manual commits from each group)
    • Anyone can edit the yaml file to indicate source location

MGI Meeting Follow Up

  • Attribution - moving forward on implementation for that
    • Seth/Chris need to capture this info in the model
    • Started a new file in GO github to reference groups that different curators associate with
    • We want to go more granular than just a group and capture specific projects within a group, a la UCL (BHF, Parkinson's, etc.)
    • Perhaps not as granular as a meeting, though (Some GO_REFs have been used for that sort of thing, but would be good to review how these have been used.)

LEGO Relations

  • New relations needed:
    • removes_input
    • directionality for causally_upstream_of_or_within and causally_upstream_of
      • GH tickets have been created to request these relations
  • There are still issues on how to handle 'regulates' relations in GO
    • David OS has a new document on this
    • How the terms are defined and how the relations are used in LEGO need to be consistent
    • Contrast regulation of a molecular level process vs regulation of a biological quality