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

• ftp://ftp-exchange.embl-heidelberg.de/pub/exchange/henrich/bilateria/2008_03_EBI.pdf

• 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.