Integrating hierarchical controlled vocabularies with OWL ontology: A case study from the domain of molecular interactions

Davis, M., Newman, A., Khan, I., Hunter, J. and Ragan, M. A. (2007). Integrating hierarchical controlled vocabularies with OWL ontology: A case study from the domain of molecular interactions. In: A. Brazma, S. Miyano and T. Akutsu, Proceedings of the 6th Asia Pacific Bioinformatics Conference. 6th Asia Pacific Bioinformatics Conference (APBC'08), Kyoto, Japan, (145-154). 14-17 January 2008.

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Author Davis, M.
Newman, A.
Khan, I.
Hunter, J.
Ragan, M. A.
Title of paper Integrating hierarchical controlled vocabularies with OWL ontology: A case study from the domain of molecular interactions
Conference name 6th Asia Pacific Bioinformatics Conference (APBC'08)
Conference location Kyoto, Japan
Conference dates 14-17 January 2008
Proceedings title Proceedings of the 6th Asia Pacific Bioinformatics Conference
Journal name Series on Advances in Bioinformatics and Computational Biology
Place of Publication London, U.K.
Publisher Imperial College Press
Publication Year 2007
Sub-type Fully published paper
Open Access Status File (Author Post-print)
ISBN 978-1-84816-108-5
ISSN 1751-6404
Editor A. Brazma
S. Miyano
T. Akutsu
Volume 6
Start page 145
End page 154
Total pages 10
Language eng
Abstract/Summary Many efforts at standardising terminologies within the biological domain have resulted in the construction of hierarchical controlled vocabularies that capture domain knowledge. Vocabularies, such as the PSI-MI vocabulary, capture both deep and extensive domain knowledge, in the OBO (Open Biomedical Ontologies) format. However hierarchical vocabularies, such as PSI-MI which are represented in OBO, only represent simple parent-child relationships between terms. By contrast, ontologies constructed using the Web Ontology Language (OWL), such as BioPax, define many richer types of relationships between terms. OWL provides a semantically rich structured language for expressing classes and sub-classes of entities and properties, relationships between them and domain-specific rules or axioms that can be applied to extract new information through semantic inferencing. In order to fully exploit the domain knowledge inherent in domain-specific controlled vocabularies, they need to be represented as OWL-DL ontologies, rather than in formats such as OBO. In this paper, we describe a method for converting OBO vocabularies into OWL and class instances represented as OWL-RDF triples. This approach preserves the hierarchical arrangement of the domain knowledge whilst also making the underlying parent-child relationships available to inferencing engines. This approach also has clear advantages over existing methods which incorporate terms from external controlled vocabularies as literals stripped of the context associated with their place in the hierarchy. By preserving this context, we enable machine inferencing over the ordered domain knowledge captured in OBO controlled vocabularies
Subjects 280000 Information, Computing and Communication Sciences
250000 Chemical Sciences
270000 Biological Sciences
060102 Bioinformatics
080707 Organisation of Information and Knowledge Resources
890205 Information Processing Services (incl. Data Entry and Capture)
970106 Expanding Knowledge in the Biological Sciences
Keyword Web Ontology Language (OWL)
Language structure
Hierarchical controlled vocabularies
Molecular interactions
Q-Index Code E1
Q-Index Status Confirmed Code
Additional Notes In series on 'Advances in Bioinformatics and Computational Biology', Volume 6.

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Created: Tue, 17 Jun 2008, 01:50:37 EST by Mr Christopher Davoren on behalf of School of Information Technol and Elec Engineering