Oregon GO Consortium Meeting

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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)

Ontology Content Development

Work in progress

1. Ongoing quality control using reasoner-generated reports.(Chris, David, Tanya)
2. Biological Signaling (Jen)
3. Lung development (David)
4. Organization and Biogenesis (David, Jane, Midori, Tanya)
5. Internal cross-product implementation (Chris, David, Jane, Jen, Midori, Tanya)

Ontology development discussion topics

1. Proposal to add process-specific function terms so that part_of links can be made between function and process (Chris, David, Tanya)
2. 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.)
3. Chaperones: revisited many years later
4. '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

OBO-Edit

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

Organization/Management

1. Ontology development timeline (Ontology development team)
2. SF status update (Midori)

General Annotation Issues

Evidence Codes

1. IC from ISS?
   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)

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're just waiting out the notification period. It will be closed well before the meeting. -midori

Web presence, Outreach and User Advocacy

Outreach

Short reports from two or three staff members on major annotation outreach events since the last consortium meeting. (15 minutes)

Report from Jane Lomax on Help Desk stats, and other user advocacy progress since the last consortium meeting. (10 minutes)

GO Papers, Publications and Presentations

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

Other items

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

Consortium meetings

• Next GOC meeting

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