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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: Fri Jan 19 19:57:42 GMT 2007

Links: Curation

We view the curation of ontologies in the context of e-Science as encompassing creating and publishing ontologies, as well as tracking changes and maintaining consistency in the ontologies after publication. A related issue is the maintenance of ontological annotations assigned to data under a given ontology, as the ontology may change after a term has been used as an annotation and therefore one may wish for the annotation to be updated as well. As the use of ontologies widens, the problems of tracking versions, and the changes between versions, and of reconciling differences in conceputal modelling arise. Our solution is to re-engineer the COBrA ontology editor and mapping tool as a Protege plug-in, and to implement an ontology management server.

It has been noted  that changes to scientific data archives are accretive – most changes are additive – although deletion and modification also occur. Scientific data is typically structured hierarchically, allowing a hierarchical key structure to be exploited in archiving changes to the data. Managing versions of a data resource can be performed on the basis of diffs (i.e. by recording the editing steps that cause the change). However, there are advantages for an approach where all objects have an associated timestamp. The central notions of hierarchical organisation, objects and timestamps (Buneman, Fan et al. 2001, 2002) also apply to ontologies and ontology management, and this is the approach we plan to adopt. Given the problems noted by Noy et al. (2003) with the simple diff approach, our approach will also be structure-based. We shall identify types of ontological changes that occur in practice, taking the procedures used in practice, e.g. by the Gene Ontology, as a starting point. As we do not assume that ontologies will make use of formalisms such as Description Logic, our approach is not reliant on the widespread uptake of this particular logic. However, we will exploit any formalism that is associated with an ontology, which may be DL or first-order logic.