LEGO August 29, 2016

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Training and Documentation

UK Training Session

USC Training Session

  • Looks like the best day is 2016-11-07, the Monday after the consortium meeting
  • Paul T. looking into arranging a room at USC.


  • Some comments and edits made to the Quick Start guide
  • Any more comments on Quick Start Guide?

Software Updates

Updates to UI

NEO Overview and GPI Files

  • Questions, issues still to be sorted out?
    • We have entries for:
      • Genes
      • Proteins
      • Transcripts
      • ncRNAs
      • Protein Complexes
    • How should protein complexes be represented?
  • Next steps - documentation of contents, communication of pipeline to other groups

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