2012 PAINT

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PAINT User Guide: http://wiki.geneontology.org/index.php/PAINT_User_Guide


Preliminary agenda

DAY 1 9am-noon

  • Introduction to evolution of gene families and function (Paul)
  • PAINT: overview and general utilities (Huaiyu)


DAY 1 1pm-5pm

  • Walk though an example: PTHR10003 (CCS)
  • The goal is to get everyone familiar with the PAINT tool.


BREAK

  • First common example: PTHR19443 (Hexokinase)
    • MF annotation
    • MF discussion


    • CC annotation
    • CC discussion
    • BP annotation
    • BP discussion



DAY 2 9am

  • Walk through more complicated examples
    • PTHR11537 (Kv channel)
    • PTHR11254 (Ubiquitin protein ligase)
    • PTHR19384 Nitric oxide synthase
      • Excessive downstream processes



  • Dinner at Huaiyu's house in Palo Alto. Please plan accordingly.

DAY 3 & DAY 4

  • Everyone works on example trees.
  • One family each half day, 4 examples total
  • Leave an hour at the end of each half day for wrap-up discussion. One participant should present the annotation and lead the discussion.



List of possible examples for the workshop

  • Gene duplications
    • PTHR19957 (Syntaxin) - similar as above.
  • Transcription factors
    • PTHR11829 (Transcription factor)
  • Very complicated families
    • PTHR11256 (bcl-2) - Too many GO terms. How to prioritize?
  • ??
    • PTHR13697 (Phosphofructokinase)
    • PTHR11361? Example of loss of function / stop propagation / add new function without loss

Pascale

    • Leukotriene PTHR12050

Part of BP discussion:

  • Annotations to be cautious about (Pascale)
    • Regulation of tyrosine hydroxylase activity
    • Activation of transcription factors, including production of downstream proteins (interleukins)



Action Items

Created on 12/13/2012. Names in parenthesis are in charge of the item.

  • Curation (Pascale)
    • Tracking families curated or being curated
      • wiki page
      • set up svn locally, so curators will create a folder in svn when a family is being curated
      • PAINT tool will add the ability to handle this in svn
    • Update user guide (Huaiyu)
      • Reopen curated families from svn (checkout from svn, open, curate and upload back to svn)
      • svn check in procedure (Paul updated this part)
    • Report feedback on issues (Rama)
      • ontology issues
      • annotation issues
    • Biweekly conference calls (Huaiyu will sent reminders)
    • Discussion list (Donghui) - Discussion will be on either paint_discuss or go_discuss

go-discuss@lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/go-discuss

  • PAINT tool - Suzi and Brentley

Bug track and new feature requests should be done in JIRA. The current ones on google doc should be migrated to JIRA also.