Oregon GO Consortium Meeting: Difference between revisions

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'''1:00-2:30''' <br>(9pm-10.30pm BST)
'''1:00-2:30''' <br>(9pm-10.30pm BST)


Watching remote people: Peter D'Eustachio
Watching remote people: '''Peter D'Eustachio'''


===OBO-Edit===
===OBO-Edit===

Revision as of 02:46, 30 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
(4:30- 5:00pm BST)

Coffee, Introductions

9:00-10:30
(5:00- 6:30pm BST)

OBO-Edit2.0 Tutorial and Demo (Chris, Amina, OBO-Edit Working Group)

  • Working with Cross-products in OBO-Edit (Chris)
    • Finding xp terms, searching, recognizing, constructing and manipulating xps
    • Using the xp panel in the Text Editor
    • Demo using the "internal" xps to be added to the live GO
  • OBO-Edit Working Group Meeting

10:30-10:45
(6:30- 6:45pm BST)

Coffee Break

10:45-12:00
(6:45- 8:00pm BST)

Working sessions: 1) David Hill, Tanya and Amina 2) OBO-Edit Working Group Members

12:00-1:30
(8pm-9.30pm BST)

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


1:30-1:45
(9.30pm-9.45pm BST)

Reference Genomes Update

Brief report of Ref Genome Progress (Pascale)

Watching remote people: Tanya Berardini


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


1:45-2:00
(9.45pm-10pm BST)

GO Clinics Update (Jane -remote-)

slides

Watching remote people: Tanya Berardini


2:00-2:30
(10pm-10.30pm BST)

Annotation Metrics (Judy?)

Watching remote people: Tanya Berardini

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


2:30-3:00
(10.30pm-11pm BST)

Coffee Break


3:00-4:30
(11pm-12.30pm BST)

'binding' issues

Watching remote people: Stan Laulederkind

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

Evidence Codes

Watching remote people: Lakshmi Pillai

  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 (Chris)

Watching remote people: Amina Abdulla

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

Official documentation: Annotation_Cross_Products

Column 17 (Chris)

Watching remote people: Stan Laulederkind

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 Official documentation: GAF_Col17_GeneProducts

SO update

Watching remote people: Donghui Li

Progress report on Sequence Ontology (Karen E)

4:30-5:00
(12.30am-1am BST)

PAINT demo

7:00PM

Dinner at Mekalas

TUESDAY March 31

8:30-10:30
(4.30pm-6.30pm BST)

Ontology Content Development

Organization/Management

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

Work in progress

Watching remote people: Susan Tweedie

  1. Ongoing quality control using reasoner-generated reports.(10 mins, Chris, David, Tanya)[1]
  2. Lung development (15 mins, David)
  3. Biological Signaling (5 mins, Jen -remote-) slides

Watching remote people: Michelle Gwinn-Giglio

  1. Organization and Biogenesis (15 mins, David, Jane -remote-, Midori -remote-, Tanya)
  2. Internal cross-product implementation (10 mins, Chris, David, Jane-remote-, Jen-remote-, Midori-remote-, Tanya)
  3. 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
(6.30pm-7pm BST)

Break


11:00-12:00
(7pm-8pm BST)

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) Watching remote people: Stan Laulederkind
  2. Chaperones: revisited many years later (Midori will introduce topic, Rama will moderate discussion) - see introductory slides; Chaperones wiki page; SF 2560932 Watching remote people: Lakshmi Pillai
  3. 'Response to stimulus' - does the definition need to be revised? Clarify when these terms should and should not be used for annotation introductory slides (also relevant to Reference Genomes). See SF 2094943 Watching remote people: Amina Abdulla
  4. The possibility of linking terms in the OBO file to discussions in the GO wiki. This could be done to ensure increased awareness of ontology/annotation discussion topics for all curators (and interested external users). This item follows on from the 'document communication' discussion at the last GO Consortium meeting [2] (Emily will introduce topic) slides

Watching remote people: Lakshmi Pillai

12:00-12:15
(8pm-8.15pm BST)

Next GOC meeting - Fall 2009

GOC September 23-24
SAB September 25
Both at Jesus College, Cambridge, UK


12:15-1:15
(8.15pm-9.15pm BST)


Lunch - Catered at meeting room


1:00-2:30
(9pm-10.30pm BST)

Watching remote people: Peter D'Eustachio

OBO-Edit

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

Web presence, Outreach and User Advocacy

Outreach and Advocacy

  1. Short report from Emily Dimmer of GOA on the progress in introducing Swiss Institute of Bioinformatics curators to GO annotation. (5 min)
  2. Report from Jane on Help Desk stats, and other user advocacy progress since the last consortium meeting including demo of new news feed by Seth. (20 min)

Resource Usage statistics (Mike)

(15 min)

AmiGO

Amigo update and report (25 min)

GONUTS

~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.


2:30-3:00
(10.30pm-11pm BST)

Break

General Annotation Issues

3:00-5:00
(11pm-1am BST)

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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