An ontology-driven semantic mashup of gene and biological pathway information: Application to the domain of nicotine dependence

• Published in: Computers and biomedical research 2008-10, Vol.41 (5), p.752-765
• Main Authors: Sahoo, Satya S., Bodenreider, Olivier, Rutter, Joni L., Skinner, Karen J., Sheth, Amit P.
• Format: Article
• Language: English
• Subjects: Animals; Biological Science Disciplines - methods; Brain - physiology; Brain - physiopathology; Database Management Systems; Gene Regulatory Networks; Humans; Information integration; Information Storage and Retrieval - methods; Internet - organization & administration; Knowledge Bases; Neural Networks (Computer); Nicotine dependence; Ontologies; Protein Interaction Mapping - methods; Semantic mashup; Semantic web; Semantics; Systems Integration; Tobacco Use Disorder - genetics; Tobacco Use Disorder - metabolism; Vocabulary, Controlled
• ISSN: 1532-0464; 0010-4809; 1532-0480
• DOI: 10.1016/j.jbi.2008.02.006

This paper illustrates how Semantic Web technologies (especially RDF, OWL, and SPARQL) can support information integration and make it easy to create semantic mashups (semantically integrated resources). In the context of understanding the genetic basis of nicotine dependence, we integrate gene and pathway information and show how three complex biological queries can be answered by the integrated knowledge base. We use an ontology-driven approach to integrate two gene resources (Entrez Gene and HomoloGene) and three pathway resources (KEGG, Reactome and BioCyc), for five organisms, including humans. We created the Entrez Knowledge Model (EKoM), an information model in OWL for the gene resources, and integrated it with the extant BioPAX ontology designed for pathway resources. The integrated schema is populated with data from the pathway resources, publicly available in BioPAX-compatible format, and gene resources for which a population procedure was created. The SPARQL query language is used to formulate queries over the integrated knowledge base to answer the three biological queries. Simple SPARQL queries could easily identify hub genes, i.e., those genes whose gene products participate in many pathways or interact with many other gene products. The identification of the genes expressed in the brain turned out to be more difficult, due to the lack of a common identification scheme for proteins. Semantic Web technologies provide a valid framework for information integration in the life sciences. Ontology-driven integration represents a flexible, sustainable and extensible solution to the integration of large volumes of information. Additional resources, which enable the creation of mappings between information sources, are required to compensate for heterogeneity across namespaces. http://knoesis.wright.edu/research/lifesci/integration/structured_data/JBI-2008/