A semantic web approach to biological pathway data reasoning and integration

Authors:
Kei-Hoi Cheung;Peishen Qi;David Tuck;Michael Krauthammer
Affiliations:
Center for Medical Informatics, Yale University, United States and Department of Anesthesiology, Yale University, United States and Department of Genetics, Yale University, United States and Depar ...;Department of Computer Science, Yale University, United States;Department of Pathology, Yale University, United States;Department of Pathology, Yale University, United States
Venue:
Web Semantics: Science, Services and Agents on the World Wide Web
Year:
2006

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Abstract

This paper describes the use of semantic web technology and Description Logic (DL) for facilitating the integration of molecular pathway data, which is illustrated by an Web Ontology Language (OWL)-based transformation of a more complex pathway structure (Reactome) into a simpler one (HPRD). The process starts by adding OWL axioms to BioPAX, a pathway interchange standard. The axioms are designed for mapping BioPAX-formatted Reactome interactions to ''molecular binding event'' interactions, which can be easily aligned with the HPRD data. Using an automated OWL reasoner, we find overlapping and non-overlapping molecular interactions between the two pathway datasets. The paper demonstrates the potential of semantic web and its enabling technologies in biological pathway data reasoning and integration.