Open Access Highly Accessed Database

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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Citation and License

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

Published: 19 January 2012



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.


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 webcite.


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.

data integration; search engine; biological ontologies