Semantic Mashup for Nicotine Dependence Research
February 13, 2009 Leave a comment
Here’s an excellent paper by S Sahoo, O Bodenreider, JL Butter, KJ Skinner, and AP Sheth titled “An ontology-driven semantic mashup of gene and biological pathway information: Application to the domain of nicotine dependence”. From the abstract:
“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.”
The papers describes the methodology they used to create an RDF store for data related to genes and pathways associated with nicotine dependence. I was particularly interested in how they handled data extracted from the NCBI Entrez database. I’ve struggled with this myself in generated RDF data from PubChem. They developed a simple XML->RDF translator and then used OWL to provide the semantic framework for the results.
This is a good paper illustrating the advantages of using semantic technologies for data integration.