2012 PAINT: Difference between revisions

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[[Category:Workshops]]
PAINT User Guide: http://wiki.geneontology.org/index.php/PAINT_User_Guide
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Preliminary agenda
Preliminary agenda


DAY 1 AM
DAY 1 9am-noon
* Introduction to evolution (Paul)
* Introduction to evolution of gene families and function (Paul)
* PAINT: overview and general utilities (Huaiyu)
* PAINT: overview and general utilities (Huaiyu)




DAY 1 PM
DAY 1 1pm-5pm


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




BREAK
BREAK
* First common example (TBD - easy)
* First common example: PTHR19443 (Hexokinase)
** MF annotation
** MF annotation
** MF discussion
** MF discussion
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DAY 2 AM
DAY 2 9am
 
* Walk through a more complicated example
 
We need to define types of examples with specific issues: 
** Families where a member has lost a function
WE NEED TO START A TABLE with types


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


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)






*Dinner at Huaiyu's house in Palo Alto. Please plan accordingly.
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List of possible examples for the workshop
List of possible examples for the workshop


* Simple examples
* Gene duplications
**PTHR19443 (Hexokinase) - A classic example of protein families involved in metabolic pathways.
* Families with lots of duplications from the root, with new BP in recent species.
**PTHR11537 (Kv channela) - A typical example of families of ion channels, transporters and receptors with lots of gene duplications.
**PTHR19957 (Syntaxin) - similar as above.
**PTHR19957 (Syntaxin) - similar as above.
*Transcription factors
*Transcription factors
**PTHR11829 (Transcription factor)
**PTHR11829 (Transcription factor)
* Very complicated families
* Very complicated families
**PTHR11256 (blc-2) - Too many GO terms. How to prioritize?
**PTHR11256 (bcl-2) - Too many GO terms. How to prioritize?
*??
*??
**PTHR11354 (Ubiquitin protein ligase)
**PTHR13697 (Phosphofructokinase)
**PTHR11361? Example of loss of function / stop propagation / add new function without loss
**PTHR11361? Example of loss of function / stop propagation / add new function without loss


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Pascale
Pascale
** Leukotriene PTHR12050


**PTHR10454 Caspase family
**PTHR10454 Caspase family
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***PMID: 22606010
***PMID: 22606010
***http://en.wikipedia.org/wiki/Caspase
***http://en.wikipedia.org/wiki/Caspase
**PTHR19384 Nitric oxide synthase
Part of BP discussion:
***Excessive downstream processes
* 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.

Latest revision as of 10:39, 12 April 2019

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.