BEReX: Biomedical Entity-Relationship eXplorer

Bioinformatics. 2014 Jan 1;30(1):135-6. doi: 10.1093/bioinformatics/btt598. Epub 2013 Oct 21.


Summary: Biomedical Entity-Relationship eXplorer (BEReX) is a new biomedical knowledge integration, search and exploration tool. BEReX integrates eight popular databases (STRING, DrugBank, KEGG, PhamGKB, BioGRID, GO, HPRD and MSigDB) and delineates an integrated network by combining the information available from these databases. Users search the integrated network by entering key words, and BEReX returns a sub-network matching the key words. The resulting graph can be explored interactively. BEReX allows users to find the shortest paths between two remote nodes, find the most relevant drugs, diseases, pathways and so on related to the current network, expand the network by particular types of entities and relations and modify the network by removing or adding selected nodes. BEReX is implemented as a standalone Java application.

Availability and implementation: BEReX and a detailed user guide are available for download at our project Web site (

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Biomedical Technology
  • Computational Biology / methods
  • Databases, Factual
  • Humans
  • Neural Networks, Computer
  • User-Computer Interface*