Applying OWL Reasoning to Genomic Data

Abstract

Abstract:The core part of the Web Ontology Language (OWL) is based on Description Logic (DL) theory, which has been investigated for more than 25 years. OWL reasoning systems offer various DL-based inference services such as (i) checking class descriptions for consistency and automatically organizing them into classification hierarchies, (ii) checking descriptions about individuals for consistency and recognizing individuals as instances of class descriptions. These services can therefore be utilized in a variety of application domains concerned with representation of and reasoning about knowledge, for example, in biological sciences. Classification is an integral part of all biological sciences, including the new discipline of genomics. Biologists not only wish to build complex descriptions of the categories of biological molecules, but also to classify instances of new molecules against these class level descriptions. In this chapter we introduce to the non-expert reader the basics of OWL DL and its related reasoning patterns such as classification. We use a case study of building an ontology of a protein family and then classifying all members of that family from a genome using DL technology. We show how a technically straight-forward use of these technologies can have far-reaching effects in genomic science.

The Ecology of Ontologies in the Public Domain

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Calculating structural complexity in phylogenies using ancestral ontologies

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Towards a methodology for Lipoprotein Ontology

“…Sentences are instantiated (as A-boxes), using a custom designed Java program, to the lipid ontology's literature specification (sentence concept) and relations to instances of each target concept are added into the ontology. The fully instantiated ontology is reasoned over using the reasoning engine RACER [20] and its A-box query language nRQL [21]. A custom built visual query interface facilitates query navigation over instantiated concept hierarchies, object properties and the visualisation of datatype properties in the ontology.…”