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

ABSTRACT:

Objectives

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.

Methods

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 fo

SUBMITTER: Sahoo SS 

PROVIDER: S-EPMC2766186 | biostudies-literature | 2008 Oct

REPOSITORIES: biostudies-literature