BEReX: Biomedical entity-relationship explorer

Minji Jeon, Sunwon Lee, Kyubum Lee, Aik-Choon Tan, Jaewoo Kang

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

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 (http://infos.korea.ac.kr/berex).Contact: Supplementary Information: Supplementary methods and user guide are available at Bioinformatics online.

Original languageEnglish
Pages (from-to)135-136
Number of pages2
JournalBioinformatics
Volume30
Issue number1
DOIs
Publication statusPublished - 2014 Jan 1

Fingerprint

Databases
Information Services
Bioinformatics
Korea
Computational Biology
Websites
Availability
Pharmaceutical Preparations
Knowledge Integration
Vertex of a graph
Relationships
Shortest path
Expand
Java
Pathway
Drugs
Integrate
Contact
Graph in graph theory

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

BEReX : Biomedical entity-relationship explorer. / Jeon, Minji; Lee, Sunwon; Lee, Kyubum; Tan, Aik-Choon; Kang, Jaewoo.

In: Bioinformatics, Vol. 30, No. 1, 01.01.2014, p. 135-136.

Research output: Contribution to journalArticle

Jeon, Minji ; Lee, Sunwon ; Lee, Kyubum ; Tan, Aik-Choon ; Kang, Jaewoo. / BEReX : Biomedical entity-relationship explorer. In: Bioinformatics. 2014 ; Vol. 30, No. 1. pp. 135-136.
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