2012 PAINT: Difference between revisions
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[[Category:Workshops]] | |||
PAINT User Guide: http://wiki.geneontology.org/index.php/PAINT_User_Guide | PAINT User Guide: http://wiki.geneontology.org/index.php/PAINT_User_Guide | ||
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Preliminary agenda | Preliminary agenda | ||
DAY 1 | 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 | 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 ( | * First common example: PTHR19443 (Hexokinase) | ||
** MF annotation | ** MF annotation | ||
** MF discussion | ** MF discussion | ||
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---- | ---- | ||
DAY 2 | DAY 2 9am | ||
* Walk through | * 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. | |||
---- | ---- | ||
Line 61: | Line 58: | ||
List of possible examples for the workshop | List of possible examples for the workshop | ||
* | * 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 ( | **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 | **PTHR11361? Example of loss of function / stop propagation / add new function without loss | ||
---- | ---- | ||
Pascale | Pascale | ||
** Leukotriene PTHR12050 | |||
**PTHR10454 Caspase family | **PTHR10454 Caspase family | ||
Line 82: | Line 78: | ||
***PMID: 22606010 | ***PMID: 22606010 | ||
***http://en.wikipedia.org/wiki/Caspase | ***http://en.wikipedia.org/wiki/Caspase | ||
** | 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. |
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
- PTHR10454 Caspase family
- PMID: 23070001
- PMID: 22949111
- PMID: 22606010
- http://en.wikipedia.org/wiki/Caspase
- PTHR10454 Caspase family
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
- Tracking families curated or being curated
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.