Oregon GO Consortium Meeting: Difference between revisions

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(15 min)
(15 min)


'''2:30-3:00'''
Break


==Web presence, Outreach and User Advocacy==
==Web presence, Outreach and User Advocacy==

Revision as of 14:39, 19 March 2009

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Dates

March 30, 31

Venue

University of Oregon, Eugene, Oregon

Erb Memorial Union (EMU), Fir Room.

Map of campus, http://map.uoregon.edu/

Map of the EMU, http://emu.uoregon.edu/map_popup.php?x=-50&y=-50&level=main&arrow=SE

Logistics

2009 Oregon Meeting Logistics

Please add yourself to the list of registrants on the Meeting Logistics Page

Agenda

ALERT: GO Top needs to sign off on agenda prior to these meetings. If there is no action item, or discussion point proposed in advance, the meeting is not the forum for first initiating a discussion.

Action Items

Minutes from the previous meeting (Montreal)


MONDAY March 30

8:30-9:00

Coffee, Introductions


9:00-10:00

OBO_Edit2.0 Tutorial (Amina, others)

10:00-10:30

Coffee Break


10:30-12:00

OBO_Edit 2.0 Tutorial cont. (Amina, others)

12:00-1:30

Lunch - Take a walk...Get food in the EMU or local restaurants


1:30-1:45

Reference Genomes Update

Brief report of Ref Genome Progress (Pascale)

  1. action item: do we continue current method of prioritization for curation?


1:45-2:00

GO Clinics Update (Jane -remote-)

2:00-2:30

Annotation Metrics (Judy?)

  1. Action Item: What is appropriate metric for comprehensive annotation?
  2. Action item: Updates to annotation metrics table


2:30-3:00

Coffee Break


3:00-4:30

'binding' issues

  1. Binding term documentation (from Debbie)
  2. using 'binding' for annotation
  3. should it be used in cross product annotations (Jim)
  4. transfer of 'binding' term annotations via ISS/ISO??

Evidence Codes

  1. Should we IC from ISS annotations?
    1. documentation currently says IC from ISS ok
    2. this is not allowed in the requirements for PAINT (but we can change that if needed)

Column 16

Can we have a progress report and a target date to work towards? Column 16 will contain cross references to other ontologies that can be used to qualify the particular annotation. Harold's draft user doc for column 16/17 usage: File:Columns 16 and 17.doc

Column 17

Can we arrange a date to release this? Column 17 is designed to allow GO annotations to specific isoform variants that may be encoded by a specific gene due to differential splicing or alternative translational starts. Harold's draft user doc for column 16/17 usage: File:Columns 16 and 17.doc

SO update

Progress report on Sequence Ontology (Karen E)

4:30-5:00 PAINT demo

TUESDAY March 31

8:30-10:30

Ontology Content Development

Organization/Management

  1. GO_Timeline (10 mins, Midori,Ontology development team)
  2. SF status update (5 mins, Midori)

Work in progress

  1. Ongoing quality control using reasoner-generated reports.(10 mins, Chris, David, Tanya)
  2. Lung development (15 mins, David)
  3. Biological Signaling (20 mins, Jen -remote-)
  4. Organization and Biogenesis (15 mins, David, Jane -remote-, Midori -remote-, Tanya)
  5. Internal cross-product implementation (10 mins, Chris, David, Jane-remote-, Jen-remote-, Midori-remote-, Tanya)
  6. Proposal to add process-specific function terms so that part_of links can be made between function and process (30 mins, Chris, David, Tanya)

presenter in bold

10:30-11:00

Break


11:00-12:00

Ontology development discussion topics

  1. Addition of localization specific process terms? (This was discussed on the GO list after it was raised in the last reference genome jamboree but hasn't been resolved.) (David will introduce topic)
  2. Chaperones: revisited many years later (Midori will introduce topic, Rama will moderate discussion)
  3. 'Response to stimulus' - does the definition need to be revised? Clarify when these terms should and should not be used for annotation (also relevant to Reference Genomes). See SF 2094943


12:00-12:15

Next GOC meeting- Fall 2009

12:15-1:15

Lunch - Catered at meeting room


1:00-2:30

OBO-Edit

  1. OBO-Edit2 Updates (15 min)
  2. SourceForge Bugs
  3. SourceForge Feature Requests

Outreach

(15 min)

Short reports from two or three staff members on major annotation outreach events since the last consortium meeting.

Report from Jane Lomax on Help Desk stats, and other user advocacy progress since the last consortium meeting.

AmiGO, Stats ?


Resource Usage statistics (Mike)

(15 min)


2:30-3:00

Break

Web presence, Outreach and User Advocacy

Amigo update and report (25 min)

GONUTS

I would like to give a short (~20 minute) overview of GONUTS (a Gene Ontology Normal Usage Tracking System.) Some things have changed in the last year, and many improvements have been made to facilitate using GO.

DanielRenfro 10:34, 16 March 2009 (PDT)

General Annotation Issues

3:00-5:00

Annotation and ontologies

  1. substrate binding...annotation or new relationship in ontology?-Pascale spoke with Jane, ontology dev. group was looking into it?
  2. protein binding...not transferred with ISS
  3. Karen: obsolete 'ATP-dependent proteolysis': Not closed yet, why?
We were just waiting out the notification period. Now closed. -midori (march 13)

GO Database

User Support

GO Papers, Publications and Presentations

  1. review for Molecular Reproduction & Development about using GO to study development (David, Doug, Kimberly, Tanya)






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