A Semantic Web Approach to Biological Pathway Data Reasoning and Integration

Kei-Hoi Cheung, Peishen Qi, David Tuck, Michael Krauthammer


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 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.

Full Text: PDF
Type of Paper: Research Paper
Show BibTex format: BibTeX