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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
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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.
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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.
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