Hinxton meeting 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).
These include:
* queries for gene expression (array and in situ) across shared anatomical structures and developmental time * need for pathway mapping and inference across species * need for annotation source that's multispecies for use in submission tools * need for validated mappings between ontologies that can be used by databases and applications that are not single species - MMIA currently provides these.
- 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
- 6. Funding
There are two possible sources of funding identified
* an unsolicited R01 * EC funding. This will be conditional on use, rather than solely development of an ontology.
AI: Helen and Bernard will look into EC funding sources (ICAT) AI: Suzi will look into submitting an R01 to develop the MCRA and do some work on CARO to support this.