Difference between revisions of "Hinxton meeting March 2008"

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* Bernard de Bono
 
* Bernard de Bono
 +
 +
=== Discussion ===
 +
 +
The presentations focussed on:
 +
 +
*  the need and use cases for a cross species anatomy ontology for annotation and analysis purposes (Helen, Thorsten, Johnathan, Bernard)
 +
 +
*  CARO state of the art and experiences extending CARO  (David, Thorsten)
 +
 +
*  Evaluation of CARO, Bilateria and MMIA against presented use cases (Helen, Johnathan, Thorsten, David)
  
 
=== Action Items ===
 
=== Action Items ===
 +
 +
* 1. Generate a list of developmental process terms and submit these to the Gene Ontology for inclusion
 +
 +
E.g. delamination
 +
 +
AI:Johnathan, David, Thorsten
 +
 +
* 2. Development of a common methodology to represent (anatomical) homology groups a David and Thorsten have approached this in a similar way already. David suggested that the FMA relations be condensed and used.
 +
 +
AI:David will generate an OBO file containing his modelling strategy
 +
 +
* 3. Development of a Most Recent Common Ancestor Anatomy (MRCA) Ontology
 +
 +
* 4. FMA update model.
 +
 +
AI: The conversion of the FMA to OWL format is non trivial and labour intensive. Suzi will contact Onard Medino to discuss this.
 +
 +
* 5. CARO improvements
 +
 +
Thorsten had successfully used CARO to build the bilateria ontology, but it was felt that the  use of CARO by other groups would be improved if:
 +
 +
* all the definitions contained examples
 +
* an example CARO should be available extended for an example species
 +
* a manual on how to use CARO is needed (the paper helps)
 +
* the FMA is a good example of definitions plus examples.
 +
* synonyms would be useful
 +
* epithelial cell could be removed - it's duplicate with the Cell Ontology
 +
* CARO doesn't deal with function and therefore organ is not present. David suggested that an  abstract class function could be added to help with refining the middle part of CARO
 +
* DS and JB will work on defining differentia (labels that would want to attach to a tissue) such as the boundary types that could be included in CARO
 +
* communication of any proposed changes should be done by the obo-anatomy list so that all are aware of proposed changes
 +
  
 
=== Shared Materials ===
 
=== Shared Materials ===

Revision as of 03:27, 31 March 2008

Attendees

  • Michael Ashburner, Cambridge University
  • Johnathan Bard, Edinburgh University
  • Bernard de Bono, EBI
  • Thorsten Henrich, EMBL
  • Suzi Lewis, LBL
  • Jane Lomax, EBI
  • James Malone, EBI
  • David Osumi-Sutherland, Cambridge University
  • Helen Parkinson, EBI
  • Monte Westerfield, Zfin

Agenda

  • Johnathan Bard - Minimal Anatomy Ontology
  • Thorsten Henrich - The Bilateria Ontology
  • David Osumi-Sutherland
  • Helen Parkinson

http://www.bioontology.org/wiki/index.php/Image:Caro_hinxton_2008.ppt#filelinks

  • Bernard de Bono

Discussion

The presentations focussed on:

  • the need and use cases for a cross species anatomy ontology for annotation and analysis purposes (Helen, Thorsten, Johnathan, Bernard)
  • CARO state of the art and experiences extending CARO (David, Thorsten)
  • Evaluation of CARO, Bilateria and MMIA against presented use cases (Helen, Johnathan, Thorsten, David)

Action Items

  • 1. Generate a list of developmental process terms and submit these to the Gene Ontology for inclusion

E.g. delamination

AI:Johnathan, David, Thorsten

  • 2. Development of a common methodology to represent (anatomical) homology groups a David and Thorsten have approached this in a similar way already. David suggested that the FMA relations be condensed and used.

AI:David will generate an OBO file containing his modelling strategy

  • 3. Development of a Most Recent Common Ancestor Anatomy (MRCA) Ontology
  • 4. FMA update model.

AI: The conversion of the FMA to OWL format is non trivial and labour intensive. Suzi will contact Onard Medino to discuss this.

  • 5. CARO improvements

Thorsten had successfully used CARO to build the bilateria ontology, but it was felt that the use of CARO by other groups would be improved if: 

* all the definitions contained examples
* an example CARO should be available extended for an example species
* a manual on how to use CARO is needed (the paper helps)
* the FMA is a good example of definitions plus examples.
* synonyms would be useful
* epithelial cell could be removed - it's duplicate with the Cell Ontology
* CARO doesn't deal with function and therefore organ is not present. David suggested that an  abstract class function could be added to help with refining the middle part of CARO
* DS and JB will work on defining differentia (labels that would want to attach to a tissue) such as the boundary types that could be included in CARO
* communication of any proposed changes should be done by the obo-anatomy list so that all are aware of proposed changes

Shared Materials

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