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Stuart Aitken
Email: stuart@aiai.ed.ac.uk
Yin Chen
Email: ychen3@inf.ed.ac.uk

Artificial Intelligence Applications Institute
The University of Edinburgh
Appleton Tower
Crichton St
Edinburgh EH8 9LE
United Kingdom

Updated: Thu Nov 22 17:43:39 GMT 2007

COBrA-CT: An Ontology Curation Tool

COBrA-CT is supported by the BBSRC under the e-Science programme, starting 1/10/2005. The project is led by Prof Bonnie Webber and Prof Wenfei Fan, School of Informatics,and Prof Jonathan Bard, Biomedical Sciences, University of Edinburgh.

The COBrA-CT project is addressing the re-formatting, editing and version management problems that arise when bio-ontologies are converted to the Web Ontology Language (OWL).

COBrA-CT provides the following tools:

  • the OBO Explorer and Ontology Metadata editors for OWL format bio-ontologies;
  • the COBrA-CT Version Manager application; providing access to
  • the COBrA-CT Ontology Server;

Data curation is important for many scientific communities and in standards initiatives, and curation has been recognised as a priority for e-Science. Ontologies are of central importance in curation, as only by defining the meaning of terms can the underlying concepts be clarified and agreed upon among the research community, and used consistently for annotating data. Ontologies themselves change and so can be considered to be the objects of curation.

A consistent, shared ontology is of critical importance to the sharing of knowledge, and has long-term value in supporting a systems-level approach to biology. For example, the Gene Ontology is in widespread use for data mining and data visualisation, and has great potential for further integration of data across the different levels of biological granularity. Ontologies have also been identified as key resources in numerous e-Science projects, including AstroGrid , MyGrid and the Advanced Knowledge Technologies IRC.

However, ontologies are not static: they must change to reflect changes in science, to adapt to new uses and new encodings, to broaden their community or to remedy flaws. We address the re-formatting, editing and version management problems that arise when bio-ontologies are converted to OWL. OWL provides powerful knowledge representation features and is supported by tools and reasoners that can be usefully exploited by bioinformaticians and biologists. In order to have a stable platform for the proposed ontology management server, and to make use of e-Science infrastructure, we have chosen the OGSA-DAI Grid middleware for both client and server.