Difference between revisions of "PAINT 2014 Summer Jamboree Kickoff Meeting Logistics"

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(Discussion and Action Items)
(Discussion and Action Items)
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*: '''ACTION ITEM''' (Karen) - Update the PAINT User Guide with info about committing an "In Progress" family (both SVN details and philosophy), include link to web view of SVN log messages, and send out an email to let everyone know.
 
*: '''ACTION ITEM''' (Karen) - Update the PAINT User Guide with info about committing an "In Progress" family (both SVN details and philosophy), include link to web view of SVN log messages, and send out an email to let everyone know.
 
*: '''ACTION ITEM''' (Suzi/Paul) - Update/modify the upcoming Jenkins report so that it will include previous commit messages, so that curators will be able to see the "in progress" log note in the web viewer for the SVN repository.
 
*: '''ACTION ITEM''' (Suzi/Paul) - Update/modify the upcoming Jenkins report so that it will include previous commit messages, so that curators will be able to see the "in progress" log note in the web viewer for the SVN repository.
 +
* PTHR11559 - Huaiyu brought up a question about general function vs. specific function. The family is a carboxylesterase family. One clade has cholinesterase genes. Within that clade, there is another clade that are acetylcholinesterase genes, which have more specific molecular function. One cholinesterase gene is annotated with acetylcholinesterase activity. However, the gene also has other cholinesterase activity. The tree shows clearly that the acetylcholinesterase specificity is gained during evolution.
 +
*: We agreed that this is something that we need to discuss with the annotation group.
 +
*: The specificity is more obvious in context of the tree.
  
 
'''Other Action Items'''
 
'''Other Action Items'''

Revision as of 09:33, 29 July 2014

Dates

  • July 28-31, 2014

Hotels

Five hotels are within a 15-30 minute walk to the meeting venue. Ordered below by price per night, lowest to highest.

  1. Hotel California
  2. Cardinal Hotel
  3. Stanford Terrace Inn
  4. Sheraton Palo Alto Hotel
  5. Westin Palo Alto

Venue

3165 Porter Dr, Palo Alto, CA
Room 1118 (downstairs)

Porter Drive is not on campus, it is off of Page Mill Road.

There is plenty of free parking in the front and rear of the building.

Agenda

Monday, July 28th

9:00am - 12:00pm

Introduction

12:00-1:30pm

Lunch

1:30pm - 5:30pm

Jamboree

Discussion and Action Items

Discussion of specific Panther families

  • PTHR13348 - Li brought up a question for PTHR13348 where the Annotation tab is showing a single ID in the with field for the "protein binding" annotation even though there are actually three ID's listed in the with field in MGI's annotation. Suzi explained that this is a parsing issue that the with field is so irregular that when there are more than one with ID's for a single annotated gene with the same reference, only one is displayed. This is not trivial to change. We agreed to accept this as an issue to be aware of as is.
  • PTHR24073 - Karen brought up a question about this family, which is the Rab GTPase superfamily. The family is huge (>2700 sequences) with a duplication node near the top. The majority of the nodes immediately below the duplication node clearly represent major classes of Rab proteins, e.g. Rab2's, Rab21's, Ift27's, Ift22's. Having scanned through the tree and annotated genes, in some clades, there is experimental evidence for "GTPase activity". However, in others, there is only evidence for "GTP binding" and/or "GDP binding". Karen asked about how to handle this family, specifically the fact that it is so big that she is confident about only a few subclades, not about all of them.
    We agreed that for huge families like these, we can do an "in progress" commit, using a specific message in the SVN commit log.
    We discussed what is the simplest explanation for GTPase activity in many of these clades, though it is not shown in all of them. Paul urged strongly to go ahead and propagate the "GTPase activity" MF term to the root of the tree. While this may be inappropriate for some subclades, let's go ahead and do it, and as Karen and/or other curators work through various subclades, and we get feedback from MOD and other curators, we can block propagation of this term to appropriate clades as appropriate.
    ACTION ITEM (Karen) - Update the PAINT User Guide with info about committing an "In Progress" family (both SVN details and philosophy), include link to web view of SVN log messages, and send out an email to let everyone know.
    ACTION ITEM (Suzi/Paul) - Update/modify the upcoming Jenkins report so that it will include previous commit messages, so that curators will be able to see the "in progress" log note in the web viewer for the SVN repository.
  • PTHR11559 - Huaiyu brought up a question about general function vs. specific function. The family is a carboxylesterase family. One clade has cholinesterase genes. Within that clade, there is another clade that are acetylcholinesterase genes, which have more specific molecular function. One cholinesterase gene is annotated with acetylcholinesterase activity. However, the gene also has other cholinesterase activity. The tree shows clearly that the acetylcholinesterase specificity is gained during evolution.
    We agreed that this is something that we need to discuss with the annotation group.
    The specificity is more obvious in context of the tree.

Other Action Items

  • ACTION ITEM (Suzi) - In PAINT, clicking on links within the Annotations tab should NOT recenter, but clicking on a term in the Annotation matrix should recenter to the LCA
  • ACTION ITEM (Suzi) - send out contact info for people to let know about when you see a bunch of partial sequences

Tuesday, July 29th

9:00pm - 10:00pm

Daily kickoff discussion

10:00am - 12:00pm

Jamboree

12:00-1:30pm

Lunch

1:30pm - 5:30pm

Jamboree

Wednesday, July 30th

9:00pm - 10:00pm

Daily kickoff discussion

10:00am - 12:00pm

Jamboree

12:00-1:30pm

Lunch

1:30pm - 5:30pm

Jamboree

Thursday, July 31st

9:00pm - 10:00pm

Daily kickoff discussion

10:00am - 12:00pm

Jamboree

12:00-1:30pm

Lunch

1:30pm - 4:30pm

Closing and wrap up

Participants

Name Organization

Li Ni

MGI, JAX

Suzi Lewis

LBL

Moni Munoz-Torres

LBL

Paul Thomas

USC

Judy Blake

MGI, JAX

Karen Christie

MGI, JAX

Kimberley Van Auken

WormBase, Caltech

Rama Balakrishnan

SGD, Stanford

Pascale Gaudet

SIB

Huaiyu Mi

USC

Marc Feuermann

SIB

Remote Attendees

  • We will have Webex to share our presentations/desktop. I will send the invitation to the go-discuss mailing list.
  • For voice/audio we will use the GO Conference line (1866 953 9688, code: 801561#).