Manager 18February2015

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Agenda

  • Future development of Protein2GO
    • What are the plans?

Minutes

  • On call: Chris, Huaiyu, Paola, Rama, Kimberly, Judy, David, Paul T., Pascale
  • CAF/CAT Discussion
    • Kimberly, Rama:
      • have some questions about how to move forward with development of Protein2GO
      • how best to coordinate with UniProt, Tony
      • there are both technical issues and annotation issues
    • Chris:
      • Rachael was our tracker, but she is no longer at UniProt and a GO manager.
      • need a tracker that GO managers can all see
      • need to develop annotation extension feedback
      • also need a high level review of where things stand with Protein2GO migration on the whole
    • Chris, Judy:
      • in a holding pattern right now wrt Protein2GO migration
    • Rama:
      • more integrated workflow for some groups makes moving to a GO-specific curation tool more difficult
    • David:
      • one area for tool development: good idea to have pre-seeded annotation extension options
      • e.g. transcription - input gene, output transcript or catalytic activity - input enzyme, output substrate
    • Chris:
      • would be good to add these use cases to Noctua tracker
    • Summary and Action Items:
      • holding pattern with Protein2GO migration, but there will be requirements still coming in for current users
      • where to put these? what tracker to use?
      • consult with Tony - can we use github and put code, requests there?
    • CAF/CAT big picture
      • review doc from initial requirements gathering
      • get in touch with other groups about requirements to assess where things currently stand wrt workflow and migrating to a CAF/CAT
  • Moving AmiGO to the cloud
    • Rama, Chris:
      • priority to move AmiGO to the cloud for better accessibility
      • set up a meeting with Stuart and Berkeley
  • Files - behind-the-scenes organization
    • Rama, Chris:
      • xrefs_abbs file
      • old, stanza-type file still supported
      • new source file lives in github; yaml format; handles more detailed metadata
      • source file no longer in SVN repository (SVN holds derived production version)
      • if people need to add a new namespace - can ask Seth and Chris for now
      • in long run, github is actually easier for management (can edit via web interface)
    • David:
      • can we have a directory/table to tell users where editable files are located
    • Chris:
      • in the xrefs_abb header, there is information about where to edit the file
    • David:
      • which files, how they’re used, where they live - big picture diagram is helpful
    • Chris:
      • could give periodic updates on behind-the-scenes organization
    • Rama:
      • would be good to explain how things work - GAFs, Jenkins scripts, Mike’s scripts, GO slims
      • have a consortium-wide call in March to talk about these things
  • Priorities for Remainder of Grant Cycle
    • Judy:
      • PI meeting in Hinxton
      • met with Alex and Claire, also Helen
      • discussed format of next grant proposal
    • Paul T:
      • what do we feel we have to accomplish before next grant submission
      • what does that mean for priorities and allocation of resources
      • still need to work out specifics
    • Judy:
      • need to continue to put a lot of effort into the common annotation environment
      • need to work on user experience, interface
      • will probably have additional meetings to address these issues
      • rearrange Trello boards accordingly
  • PAINT curation
    • Pascale:
      • still problems using PAINT, accessing database
      • can we have more frequent checks for potential connection errors