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

Randall C Willis1, Christopher W.V. Hogue1

1 The Blueprint Initiative, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 8.9
DOI:  10.1002/0471250953.bi0809s12
Online Posting Date:  January, 2006
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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

     
 
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Table of Contents

  • Basic Protocol 1: The BIND Interface: Getting Started
  • Basic Protocol 2: Searching BIND Using Text Queries, Identifier Function, or Molecule Short Label
  • Basic Protocol 3: Searching BIND Using the Field‐Specific Function
  • Basic Protocol 4: Searching BIND by Sequence: BINDBlast
  • Basic Protocol 5: Searching BIND by Browsing the Statistics Page
  • Basic Protocol 6: Viewing BIND Search Results
  • Basic Protocol 7: Viewing Interaction Records
  • Basic Protocol 8: Exporting BIND Search Results for Use with Other Software
  • Basic Protocol 9: Visualizing Interactions Using the BIND Interaction Viewer (BIV)
  • Basic Protocol 10: Exporting BIND Interaction Data for Viewing with Cytoscape or Cn3D
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

   Alfarano, C., Andrade, C.E., Anthony, K., Bahroos, N., Bajec, M., Bantoft, K., Betel, D., Bobechko, B., Boutilier, K., Burgess, E., Buzadzija, K., Cavero, R., D'Abreo, C., Donaldson, I., Dorairajoo, D., Dumontier, M.J., Dumontier, M.R., Earles, V., Farrall, R., Feldman, H., Garderman, E., Gong, Y., Gonzaga, R., Grytsan, V., Gryz, E., Gu, V., Haldorsen, E., Halupa, A., Haw, R., Hrvojic, A., Hurrell, L., Isserlin, R., Jack, F., Juma, F., Khan, A., Kon, T., Konopinsky, S., Le, V., Lee, E., Ling, S., Magidin, M., Moniakis, J., Montojo, J., Moore, S., Muskat, B., Ng, I., Paraiso, J.P., Parker, B., Pintilie, G., Pirone, R., Salama, J.J., Sgro, S., Shan, T., Shu, Y., Siew, J., Skinner, D., Snyder, K., Stasiuk, R., Strumpf, D., Tuekam, B., Tao, S., Wang, Z., White, M., Willis, R., Wolting, C., Wong, S., Wrong, A., Xin, C., Yao, R., Yates, B., Zhang, S., Zheng, K., Pawson, T., Ouellette, B.F., and Hogue, C.W. 2005. The Biomolecular Interaction Network Database and related tools 2005 update. Nucl. Acids Res. 33:D418‐424.
   Gilbert, D. 2005. Biomolecular interaction network database. Brief. Bioinform. 6:194‐198.
   Hermjakob, H., Montecchi‐Palazzi, L., Lewington, C., Mudali, S., Kerrien, S., Orchard, S., Vingron, M., Roechert, B., Roepstorff, P., Valencia, A., Margalit, H., Armstrong, J., Bairoch, A., Cesareni, G., Sherman, D., and Apweiler, R. 2004. IntAct: An open source molecular interaction database. Nucl. Acids Res. 32:D452‐D455.
   Salama, J.J., Donaldson, I., and Hogue, C.W. 2001‐2002. Automatic annotation of BIND molecular interactions from three‐dimensional structures. Biopolymers 61:111‐120.
   Xenarios, I., Salwinski, L., Duan, X.J., Higney, P., Kim, S., and Eisenberg, D. 2002. DIP: The Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions. Nucl. Acids Res. 30:303‐305.
   Zanzoni, A., Montecchi‐Palazzi, L., Quondam, M., Ausiello, G., Helmer‐Citterich, M., and Cesareni, G. 2002. MINT: A Molecular INTeraction database. FEBS Lett. 513:135‐140.
Internet Resources
   http://bind.ca
  Web site for the Biomolecular Interaction Network Database (BIND).
   http://mint.bio.uniroma2.it/mint/
  Web site for the Molecular Interactions (MINT) Database.
   http://dip.doe‐mbi.ucla.edu
  Web site for the Database of Interacting Proteins (DIP).
   http://www.adobe.com
  Web site for Adobe Acrobat Reader.
   http://www.cytoscape.org
  Web site for Cytoscape.
   http://www.ebi.ac.uk/intact/index.jsp#ack
  Web site for the IntAct Project.
   http://www.java.com
  Web site for Java.
   http://www.microsoft.com
  Web site for Microsoft Office (including Excel).
   http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml
  Web site for the NCBI Structure group's Cn3D.
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