The Biomolecular Interaction Network Database and related tools 2005 update

Abstract

The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular interaction, reaction, complex and pathway information. Our aim is to curate the details about molecular interactions that arise from published experimental research and to provide this information, as well as tools to enable data analysis, freely to researchers worldwide. BIND data are curated into a comprehensive machine-readable archive of computable information and provides users with methods to discover interactions and molecular mechanisms. BIND has worked to develop new methods for visualization that amplify the underlying annotation of genes and proteins to facilitate the study of molecular interaction networks. BIND has maintained an open database policy since its inception in 1999. Data growth has proceeded at a tremendous rate, approaching over 100 000 records. New services provided include a new BIND Query and Submission interface, a Standard Object Access Protocol service and the Small Molecule Interaction Database (http://smid.blueprint.org) that allows users to determine probable small molecule binding sites of new sequences and examine conserved binding residues.

Figure 1

One view from the BIND interface showing a ‘cancer’ text query, restricting results to the BIND-Metazoa division and excluding high-throughput interactions. At the bottom, the list of pairwise interactions shows the OntoGlyph symbols which have click-through links for GO annotation details. At the top right is a list of export formats for the entire set of query results including Microsoft Excel (CSV), Cytoscape (highlighted) and PSI-Level II data files.