Difference between revisions of "CDAO"

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(Telecon, 7 March, 2007)
(Telecon, 7 March, 2007)
Line 23: Line 23:
 
What activities to do before the meeting?  Plan for development?  
 
What activities to do before the meeting?  Plan for development?  
 
# represent 4 simple test cases  
 
# represent 4 simple test cases  
** nt alignment plus tree
+
## nt alignment plus tree
** prot alignment plus tree
+
## prot alignment plus tree
** kinases with inhibitor sensitivity
+
##  kinases with inhibitor sensitivity
** worm morphologies
+
##  worm morphologies
 
# carry out operations with reasoning
 
# carry out operations with reasoning
** set and logic operations on characters and OTUs
+
## set and logic operations on characters and OTUs
** clade selection
+
## tree operations (clade selection, prune)
** other?   
+
## other?   
 
# map ontology to other representations
 
# map ontology to other representations
** NEXUS
+
## NEXUS
** neXML
+
## neXML
  
 
Other issues for meeting and for paper
 
Other issues for meeting and for paper
# what is the scope?  
+
* what is the scope?  
# How to integrate with other ontologies?  
+
* How to integrate with other ontologies?  
 
** table from 'related artefacts' exercise  
 
** table from 'related artefacts' exercise  
** genetic code as an example
+
** genetic code as a test case for integration
 +
*** requires nt aa mapping to specify code
 +
*** requires species taxonomy to assign code to species
 +
*** requires cell ontology to assign code to compartmental genome (nuc, mito, cp)
  
 
Next meeting
 
Next meeting

Revision as of 12:09, 7 March 2008

Comparative Data Analysis Ontology

The material previously on this page has been moved to CDAOManuscript.

This page is for ongoing work and contains links to supporting docs, past work, and sub-topics.

Test Data Sets

Initial Implementation

Evaluation

Meeting Notes

Telecon, 7 March, 2007

present: Francisco Prodoscimi, Julie Thompson, Enrico Pontelli, Arlin Stoltzfus

What activities to do before the meeting? Plan for development?

  1. represent 4 simple test cases
    1. nt alignment plus tree
    2. prot alignment plus tree
    3. kinases with inhibitor sensitivity
    4. worm morphologies
  2. carry out operations with reasoning
    1. set and logic operations on characters and OTUs
    2. tree operations (clade selection, prune)
    3. other?
  3. map ontology to other representations
    1. NEXUS
    2. neXML

Other issues for meeting and for paper

  • what is the scope?
  • How to integrate with other ontologies?
    • table from 'related artefacts' exercise
    • genetic code as a test case for integration
      • requires nt aa mapping to specify code
      • requires species taxonomy to assign code to species
      • requires cell ontology to assign code to compartmental genome (nuc, mito, cp)

Next meeting

  • telecon, 14 March, 10:00 EST (GM===
  • agenda
    • nt and prot test data sets (arlin)
    • protege demo (brandon)

another meeting