Unit

UNIT 8.9 Searching, Viewing, and Visualizing Data in the Biomolecular Interaction Network Database (BIND)

  1. Randall C Willis,
  2. Christopher W.V. Hogue

Published Online: 1 JAN 2006

DOI: 10.1002/0471250953.bi0809s12

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Willis, R. C. and Hogue, C. W. 2006. Searching, Viewing, and Visualizing Data in the Biomolecular Interaction Network Database (BIND). Current Protocols in Bioinformatics. 12:8.9:8.9.1–8.9.30.

Author Information

  1. The Blueprint Initiative, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada

Publication History

  1. Published Online: 1 JAN 2006
  2. Published Print: DEC 2005

Abstract

The Biomolecular Interaction Network Database (BIND) comprises data from peer-reviewed literature and direct submissions. BIND's data model was the first of its kind to be peer-reviewed prior to database development, and is now a mature standard data format spanning molecular interactions, small molecule chemical reactions, and interfaces from three-dimensional structures, pathways, and genetic interaction networks. BIND supports additional file formats to achieve compatibility with other database efforts, including the HUPO PSI Level 2. BIND's latest software spans over 2000 metadata fields and is constructed using the Java Enterprise Systems software platform. Protocols are provided for searching BIND via the Internet, as well as for viewing and exporting search results or individual records. Furthermore, a protocol is provided for visualizing biomolecular interactions within BIND or for transferring this information to the visualization tools Cytoscape and Cn3D.

Keywords:

  • BIND;
  • molecular;
  • interactions;
  • database;
  • pathways