Applying Ontology Design Patterns in Bio-ontologies

Authors:
Mikel Egaña;Alan Rector;Robert Stevens;Erick Antezana
Affiliations:
School of Computer Science, University of Manchester, UK;School of Computer Science, University of Manchester, UK;School of Computer Science, University of Manchester, UK;Department of Plant Systems Biology, VIB, Gent, Belgium and Department of Molecular Genetics, Gent University, Belgium
Venue:
EKAW '08 Proceedings of the 16th international conference on Knowledge Engineering: Practice and Patterns
Year:
2008

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Abstract

Biological knowledge has been, to date, coded by biologists in axiomatically lean bio-ontologies. To facilitate axiomatic enrichment, complex semantics can be encapsulated as Ontology Design Patterns (ODPs). These can be applied across an ontology to make the domain knowledge explicit and therefore available for computational inference. The same ODP is often required in many different parts of the same ontology and the manual construction of often complex ODP semantics is loaded with the possibility of slips, inconsistencies and other errors. To address this issue we present the Ontology PreProcessor Language (OPPL), an axiom-based language for selecting and transforming portions of OWL ontologies, offering a means for applying ODPs. Example ODPs for the common need to represent "modifiers" of independent entities are presented and one of them is used as a demonstration of how to use OPPL to apply it.