Annotation Conf. Call 2019-01-08

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Meeting URL

  • check shared GO Google calendar

Agenda

2019 Plans

Annotation Group Priorities

Annotation Review

  • Reports from pipeline
    • Manual annotations
    • Mapping files, e.g. InterPro2GO
      • Still some 'gocheck_do_not_annotate' mappings in InterPro2GO
  • Molecular Function refactor
  • Transcription
  • Annotation to regulation terms - what does GO mean by 'regulation'?
  • Other methods to identify annotations to review
    • Matrix

Metrics

  • Tracking, reporting number of publications as a measure of information content
  • Tracking changes to annotations over time

Topic-Specific Projects

  • Tie-up an loose ends for existing signaling projects
    • GPCR, JAK/STAT, Wnt (ideally a GO-CAM model for each pathway - as a template)
  • Continue with additional signaling pathways
  • Transcription
  • Protein-containing complexes

GO-CAM/Noctua

  • Continued discussion of modeling questions
  • Generation and use of templates
  • Import of Reactome pathways
  • Import of whole genomes

Documentation

  • Relations and their use in annotation and ontology development
    • gp2term relations
    • GO-CAM relations
    • new relations in ontology development, e.g. describing participants in metabolic processes

PAINT

  • Continue curation of families with at least one human gene
  • Review families with new or revised experimental annotation

Pipeline

  • Any questions or issues that groups are having?
  • Finalize specs for new gpad/gpi file formats and transition to using these two files for internal consortium data exchange
  • Literature tracking system - gather requirements
    • Track curation status of papers
    • Add comments to papers

Meetings

Conference Calls

  • Tuesdays at 8am PDT
    • 1st Tuesday: Alliance Biological Function
    • 2nd Tuesday: GO Consortium
    • 3rd Tuesday: GO-CAM Working Group
    • 4th Tuesday: GO-CAM Working Group
    • 5th Tuesday: Alliance Biological Function
  • One Zoom URL for all - https://stanford.zoom.us/j/976175422

Consortium Meetings

  • GOC meeting - Cambridge, UK April 11th - 12th (right after ISB meeting)
  • GOC meeting - Berkeley, CA October 7th - 10th ???
    • SAB
    • GO user's meeting

Working Meetings

  • Whole genome import - CA last week of January

Minutes

  • On call: Barbara, Birgit (late), Chris M., David, Dustin, Giulia, Harold, Helen, Kevin M, Kimberly, Laurent-Philippe, Li, Liz, Midori, Patrick, Petra, Rob, Ruth, Sabrina, Seth, Shur-Jen, Stacia, Stan, Suzi, Tanya

2019 Plans

Annotation Group Priorities

Annotation Review

  • We discussed the various topics and methods for and of annotation review
    • InterPro2GO mappings - need to follow-up with InterPro on the gocheck_do_not_annotate subset
    • Transcription
      • Some work still to be done here
      • Issues surrounding SO terms used; plan is to collaborate with SO on refining the ontology wrt definitions and placement of promoter and related terms
    • Process and regulation of process
      • This will likely be a big project, but we want to get the ball rolling.
      • Jim B.'s work may help here, as well as the matrix tool
      • QC/QA working group will follow-up with this

Metrics

  • Lists of papers used for annotation can be retrieved from GAFs, QuickGO
  • Tracking annotation changes over time will need to be part of our metrics going forward
  • ISB - there will be a workshop on evaluating curation database resources; metrics is part of this discussion

Topic-Specific Projects

  • Signaling
    • AI: Add documentation on annotating specific signaling pathways to the existing, more general documentation
      • Include in this documentation, GO-CAM models and templates that delineate what activities are considered part of the pathway vs regulatory or causally upstream
    • Additional pathways to consider reviewing in 2019
      • Notch, insulin
        • FlyBase has found that one difficulty in delineating pathway members is how to consider transcription factors and branched pathways
  • Protein-containing complexes
    • Protein complexes WG will re-form in 2019 and try to address the remaining outstanding issues
    • Would also be helpful to review criteria for what constitutes membership in a protein-containing complex

Pipeline

  • Literature tracking system will likely be developed in collaboration with the Alliance