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IntegromeDB: an integrated system and biological search engine

Michael Baitaluk1*, Sergey Kozhenkov1, Yulia Dubinina1 and Julia Ponomarenko12

Author Affiliations

1 San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA

2 Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA

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BMC Genomics 2012, 13:35  doi:10.1186/1471-2164-13-35

Published: 19 January 2012

Abstract

Background

With the growth of biological data in volume and heterogeneity, web search engines become key tools for researchers. However, general-purpose search engines are not specialized for the search of biological data.

Description

Here, we present an approach at developing a biological web search engine based on the Semantic Web technologies and demonstrate its implementation for retrieving gene- and protein-centered knowledge. The engine is available at http://www.integromedb.org webcite.

Conclusions

The IntegromeDB search engine allows scanning data on gene regulation, gene expression, protein-protein interactions, pathways, metagenomics, mutations, diseases, and other gene- and protein-related data that are automatically retrieved from publicly available databases and web pages using biological ontologies. To perfect the resource design and usability, we welcome and encourage community feedback.

Keywords:
data integration; search engine; biological ontologies