IntegromeDB: an integrated system and biological search engine

BMC Genomics. 2012 Jan 19;13:35. doi: 10.1186/1471-2164-13-35.


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

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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Computational Biology / methods*
  • Databases, Factual*
  • Gene Expression
  • Internet
  • Metagenomics
  • Protein Interaction Mapping
  • Proteins / genetics
  • Search Engine
  • Software


  • Proteins