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A pattern-driven approach to biomedical ontology engineering

Lookup NU author(s): Dr Jennifer Warrender, Dr Phillip Lord


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Developing ontologies can be expensive, time-consuming, as well as dificult to develop and maintain. This is especially true for more expressive and/or larger ontologies. Some ontologies are, however, relatively repetitive, reusing design patterns; building these with both generic and bespoke patterns should reduce duplication and increase reg- ularity which in turn should impact on the cost of development.Here we report on the usage of patterns applied to two biomedical ontolo- gies: firstly a novel ontology for karyotypes which has been built ground- up using a pattern based approach; and, secondly, our initial refactoring of the SIO ontology to make explicit use of patterns at development time. To enable this, we use the Tawny-OWL library which enables full- programmatic development of ontologies. We show how this approach can generate large numbers of classes from much simpler data structures which is highly beneficial within biomedical ontology engineering.

Publication metadata

Author(s): Warrender JD, Lord P

Editor(s): Adrian Paschke, Albert Burger, Paolo Romano, M. Scott Marshall, Andrea Splendiani

Publication type: Conference Proceedings (inc. Abstract)

Publication status: Published

Conference Name: Proceedings of the 6th International Workshop on Semantic Web Applications and Tools for Life Sciences

Year of Conference: 2013

ISSN: 1613-0073

Publisher: CEUR-WS


Series Title: CEUR Workshop Proceedings