Collaboration with MIT GO-Engineering: Difference between revisions
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*9:20-9:40am Marco Ramoni, Harvard Medical School | *9:20-9:40am Marco Ramoni, Harvard Medical School | ||
*9:40-10:00a Judith A. Blake, The Jackson Laboratory/ GO Consortium | *9:40-10:00a Judith A. Blake, The Jackson Laboratory/ GO Consortium | ||
Gene Ontology Overview and Perspective | "Gene Ontology Overview and Perspective" | ||
*10:00-10:20am Michael Xiang, Massachusetts Institute of Technology | *10:00-10:20am Michael Xiang, Massachusetts Institute of Technology | ||
*10:20-10:40am Chris Mungall, Lawerence Berkeley National Laboratory/ | *10:20-10:40am Chris Mungall, Lawerence Berkeley National Laboratory/ | ||
GO Consortium | GO Consortium | ||
"Building the Gene Ontology Systems" | |||
*10:40-11:10am Coffee Break | *10:40-11:10am Coffee Break | ||
*11:10-11:30am David Hill, The Jackson Laboratory/ GO Consortium | *11:10-11:30am David Hill, The Jackson Laboratory/ GO Consortium | ||
Annotating Gene Products to the Gene Ontology | "Annotating Gene Products to the Gene Ontology" | ||
*11:30-11:50am Gil Alterovitz, Harvard/ Massachusetts Institute of Technology | *11:30-11:50am Gil Alterovitz, Harvard/ Massachusetts Institute of Technology | ||
*11:50-12:10pm Jane Lomax, European Bioinformatics Institute Hinxton/ | *11:50-12:10pm Jane Lomax, European Bioinformatics Institute Hinxton/ | ||
GO Consortium | GO Consortium | ||
Recent Improvements to the Gene Ontology | "Recent Improvements to the Gene Ontology" | ||
*12:10-12:30pm Closing Remarks | *12:10-12:30pm Closing Remarks | ||
Revision as of 14:28, 12 March 2007
The MIT group has used an algorithm to label GO nodes as too general or too specific based on the structure of the graph and the amount of annotation to terms. We are collaborating with them to examine their suggestions and modify the GO as needed.
Personnel
- David Hill (GO)
- Jane Lomax (GO)
- Midori Harris (GO)
- Chris Mungall (GO)
- Judith Blake (GO)
- Mary Dolan (GO)
- Jonathan Liu (MIT)
- Gil Alterovitz (MIT)
- Marco Ramoni (MIT)
- Ming Xiang (MIT)
Requirements:
MIT group provides files to GO group for examination (done) GO group reviews file and makes notes about items to discuss (March 2) GO group conference call (March 12, 2007; 11:00 am PST, 2:00 pm EST, 6:00 pm GMT) Face-to-Face meeting at MIT (March 16)
MORNING/OPEN SESSION: Harvard Institutes of Medicine New Research Building Third Floor Rotunda
- 9:00am Opening remarks
- 9:20-9:40am Marco Ramoni, Harvard Medical School
- 9:40-10:00a Judith A. Blake, The Jackson Laboratory/ GO Consortium
"Gene Ontology Overview and Perspective"
- 10:00-10:20am Michael Xiang, Massachusetts Institute of Technology
- 10:20-10:40am Chris Mungall, Lawerence Berkeley National Laboratory/
GO Consortium "Building the Gene Ontology Systems"
- 10:40-11:10am Coffee Break
- 11:10-11:30am David Hill, The Jackson Laboratory/ GO Consortium
"Annotating Gene Products to the Gene Ontology"
- 11:30-11:50am Gil Alterovitz, Harvard/ Massachusetts Institute of Technology
- 11:50-12:10pm Jane Lomax, European Bioinformatics Institute Hinxton/
GO Consortium "Recent Improvements to the Gene Ontology"
- 12:10-12:30pm Closing Remarks
AFTERNOON/CLOSED SESSION: Harvard Institutes of Medicine New Research Building (NRB) Room 258 by Invite only
- 12:30-1:30pm Lunch
- 1:30-5:30pm REGO Workshop meeting
- 6:00-7:00pm Dinner
Generously funded in part by NHGRI and i2b2
Documents (downloadable):
- Improving the Gene Ontology - Abstract Methods
- Re-Engineering Gene Ontology manuscript
- Quantifying the Specificity of GO Terms manuscript
- Quantifying the Specificity of GO Terms supplementary info
- "Information bottleneck" graph
- Spreadsheet column descriptions
- List of "too general" nodes, Oct. 2006
- List of "too specific" nodes, Nov. 2006
- comments on "too specific" list, Nov. 2006
- List of "too general" nodes, Dec. 2006 (is_a-complete GO)
- Suggested changes, 11/26/06
- Suggested changes, 12/10/06
- Responses to 12/10/06 suggestions