Collaboration with MIT GO-Engineering: Difference between revisions
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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. | 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) | * David Hill (GO) | ||
* Jane Lomax (GO) | * Jane Lomax (GO) | ||
Line 14: | Line 14: | ||
Requirements: | Requirements: | ||
# MIT group | # 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 reviews file and makes notes about items to discuss (March 2) | ||
# GO group conference call ( | # GO group conference call (March 8, 2007; 8:00 am PST, 11:00 am EST, 4:00 pm GMT) | ||
# Face-to-Face meeting at MIT (March 16) | # Face-to-Face meeting at MIT (March 16) | ||
Documents (downloadable): | |||
*[http://www.geneontology.org/meeting/GO-MIT_March2007/Improving_the_Gene_Ontology.doc Improving the Gene Ontology - Abstract Methods] | |||
*[http://www.geneontology.org/meeting/GO-MIT_March2007/Gene_Ontology_Re-Engineering_Paper-nbt_v8_f_no_com.doc Re-Engineering Gene Ontology manuscript] | |||
*[http://www.geneontology.org/meeting/GO-MIT_March2007/Quantifying_the_Specificity_of_Gene_Ontology_Terms-supp_info.doc Quantifying the Specificity of GO Terms manuscript] | |||
*[http://www.geneontology.org/meeting/GO-MIT_March2007/Quantifying_the_Specificity_of_Gene_Ontology_Terms.doc Quantifying the Specificity of GO Terms supplementary info] | |||
*[http://www.geneontology.org/meeting/GO-MIT_March2007/Graph_showing_info_bottlenecks.png "Information bottleneck" graph] | |||
*[http://www.geneontology.org/meeting/GO-MIT_March2007/Column_descriptions.xls Spreadsheet column descriptions] | |||
*[http://www.geneontology.org/meeting/GO-MIT_March2007/Too_general_nodes_10-31-06.xls List of "too general" nodes, Oct. 2006] | |||
*[http://www.geneontology.org/meeting/GO-MIT_March2007/Too_specific_nodes_11-01-06.xls List of "too specific" nodes, Nov. 2006] | |||
*[http://www.geneontology.org/meeting/GO-MIT_March2007/Too_specific_nodes_MAH_comments.xls comments on "too specific" list, Nov. 2006] | |||
*[http://www.geneontology.org/meeting/GO-MIT_March2007/data_for_isACompleteOBO 12-7-06.xls List of "too general" nodes, Dec. 2006 (is_a-complete GO)] | |||
*[http://www.geneontology.org/meeting/GO-MIT_March2007/GO_11-26-06.pdf Suggested changes, 11/26/06] | |||
*[http://www.geneontology.org/meeting/GO-MIT_March2007/12-10-06_GO_changes.doc Suggested changes, 12/10/06] | |||
*[http://www.geneontology.org/meeting/GO-MIT_March2007/Changes_Ideas_12-06.doc Responses to 12/10/06 suggestions] |
Revision as of 09:52, 22 February 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)
- 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 8, 2007; 8:00 am PST, 11:00 am EST, 4:00 pm GMT)
- Face-to-Face meeting at MIT (March 16)
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
- 12-7-06.xls 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