Difference between revisions of "2012 PAINT"

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** Biweekly conference calls (Huaiyu will sent reminders)
** Biweekly conference calls (Huaiyu will sent reminders)
** Discussion list (Donghui) - Discussion will be on either paint_discuss or go_discuss
** 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 Brently
* PAINT tool - Suzi and Brently
Bug track and new feature requests should be done in JIRA. The current ones on google doc should be migrated to JIRA also.
Bug track and new feature requests should be done in JIRA. The current ones on google doc should be migrated to JIRA also.

Revision as of 14:29, 17 December 2012

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 (Pasqual)
    • 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 Brently

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