Biochemistry Procedure-oriented Ontology: A Case Study

Mohammed Alliheedi, Yetian Wang, Robert Mercer

Abstract

Ontologies must provide the entities, concepts, and relations required by the domain being represented. The domain of interest in this paper is the biochemistry experimental procedure. The ontology language being used is OWL-DL. OWL-DL was adopted due to its well-balanced flexibility among expressiveness (e.g., class description, cardinality restriction, etc.), completeness, and decidability. These procedures are composed of procedure steps which can be represented as sequences. Sequences are composed of totally ordered, partially ordered, and alternative subsequences. Subsequences can be represented with two relations, directlyFollows and directlyPrecedes that are used to represent sequences. Alternative subsequences can be generated by composing a oneOf function in OWL-DL, referred to it as optionalStepOf in this work, which is a simple generalization of exclusiveOR. Alkaline Agarose Gel Electrophoresis, a biochemistry procedure, is described and examples of these subsequences are provided.

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