Oregon GO Consortium Meeting: Difference between revisions
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Harold's draft user doc for column 16/17 usage: [[Image:Columns 16 and 17.doc]] | Harold's draft user doc for column 16/17 usage: [[Image:Columns 16 and 17.doc]] | ||
===Column 17=== | ====Column 17==== | ||
Can we arrange a date to release this? | Can we arrange a date to release this? |
Revision as of 20:29, 17 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
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
Brief report of Ref Genome Progress (Pascale)
- action item: do we continue current method of prioritization for curation?
1:45-2:00
GO Clinics Update (Jane -remote-)
- Action Item: How long to spend on clinic discussion??
2:00-2:30
Annotation Metrics (Judy?)
- Action Item: What is appropriate metric for comprehensive annotation?
- Action item: Updates to annotation metrics table
2:30-3:00
Coffee Break
3:00-4:30
'binding' issues
- using 'binding' for annotation
- transfer of 'binding' term annotations via ISS/ISO??
Evidence Codes
- Should we IC from ISS annotations?
- documentation currently says IC from ISS ok
- 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
4:30-5:00
PAINT demo
TUESDAY March 31
8:30-10:00
Ontology Content Development
Work in progress
- Ongoing quality control using reasoner-generated reports.(Chris, David, Tanya)
- Biological Signaling (Jen-remote-)
- Lung development (David)
- Organization and Biogenesis (David, Jane-remote-, Midori-remote-, Tanya)
- Internal cross-product implementation (Chris, David, Jane-remote-, Jen-remote-, Midori-remote-, Tanya)
10:00-10:30
Break
10:30-12:00
Ontology development discussion topics
- Proposal to add process-specific function terms so that part_of links can be made between function and process (Chris, David, Tanya)
- 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.)
- Chaperones: revisited many years later
- '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
12:00-1:00
Lunch - Catered at meeting room
1:00-2:30
OBO-Edit
- OBO-Edit2 Updates
- SourceForge Bugs
- SourceForge Feature Requests
Organization/Management
- Ontology development timeline (Ontology development team)
- SF status update (Midori)
2:30-3:00
Break
3:00-5:00
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)
=== AmiGO, Stats ?
General Annotation Issues
Annotation and ontologies
- substrate binding...annotation or new relationship in ontology?-Pascale spoke with Jane, ontology dev. group was looking into it?
- protein binding...not transferred with ISS
- Karen: obsolete 'ATP-dependent proteolysis': Not closed yet, why?
- We were just waiting out the notification period. Now closed. -midori (march 13)
GO Database
Web presence, Outreach and User Advocacy
Resource Usage statistics (Mike)
User Support
GO Papers, Publications and Presentations
- review for Molecular Reproduction & Development about using GO to study development (David, Doug, Kimberly, Tanya)
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)
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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