Difference between revisions of "Collaboration with MIT GO-Engineering"

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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.
  
Personel
+
Personnel
 
* David Hill (GO)
 
* David Hill (GO)
 
* Jane Lomax (GO)
 
* Jane Lomax (GO)
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Requirements:
 
Requirements:
  
# MIT group prvides files to GO group for examination (done)
+
# 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 (regular ontology working group time March 8, 2007; 8:00amPST, 11:00amEST, 4:00pmGMT)
+
# 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]
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*[http://www.geneontology.org/meeting/GO-MIT_March2007/Quantifying_the_Specificity_of_Gene_Ontology_Terms.doc Quantifying the Specificity of GO Terms supplementary info]
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*[http://www.geneontology.org/meeting/GO-MIT_March2007/Graph_showing_info_bottlenecks.png "Information bottleneck" graph]
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*[http://www.geneontology.org/meeting/GO-MIT_March2007/Column_descriptions.xls Spreadsheet column descriptions]
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*[http://www.geneontology.org/meeting/GO-MIT_March2007/Too_general_nodes_10-31-06.xls List of "too general" nodes, Oct. 2006]
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*[http://www.geneontology.org/meeting/GO-MIT_March2007/Too_specific_nodes_11-01-06.xls List of "too specific" nodes, Nov. 2006]
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*[http://www.geneontology.org/meeting/GO-MIT_March2007/Too_specific_nodes_MAH_comments.xls comments on "too specific" list, Nov. 2006]
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*[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)]
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*[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 05:52, 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:

  1. MIT group provides files to GO group for examination (done)
  2. GO group reviews file and makes notes about items to discuss (March 2)
  3. GO group conference call (March 8, 2007; 8:00 am PST, 11:00 am EST, 4:00 pm GMT)
  4. Face-to-Face meeting at MIT (March 16)

Documents (downloadable):