Bioinformatics Computational Biology Computational Databases

BIND

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The Biomolecular Interaction Network Database archives biomolecular interaction, complex and pathway information. A web-based system is available to query, view and submit records. BIND continues to grow with the addition of individual submissions as well as interaction data from the PDB and a number of large-scale interaction and complex mapping experiments using yeast two hybrid, mass spectrometry, genetic interactions and phage display. The BIND data specification is available as ASN.1 and XML DTD. The BIND specification has remained stable since version 2.0 in 2001. Initially, BIND was designed only to support physical/biochemical interactions. 

The user interface to BIND is web based. Currently a data entry tool allows most data in the specification to be entered and changed. The database may be queried using text from any field, or directly by accession number. An integrated Java applet has been written to visually navigate the database starting from any interaction. BIND has progressed through multiple implementation cycles, each benefiting from collaborator and community constructive feedback. 

BIND is a collection of records documenting molecular interactions, including high-throughput data submissions and hand-curated information gathered from the scientific literature.

A BIND record represents an interaction between two or more objects that is believed to occur in a living organism. A biological object can be a protein, DNA, RNA, ligand, molecular complex, gene, photon or an unclassified biological entity.

The three main data types (database records) in BIND are interaction, molecular complex and pathway. An interaction record stores a description of the binding event between two objects, A and B, which are generally molecules. 

Most of the biological information in BIND is stored in an interaction record. An object in BIND may be of type protein, DNA, RNA, small molecule, molecular complex or photon. The object may store its name, a list of name synonyms, its origin whether natural or not, where it occurs in the cell, the cell stages in which it occurs and a sequence database reference to or a full instantiation of biological sequence and 3D structure. Storing the origin with the molecule allows the description of inter-species interactions. However, the policy of the database states that such cross-species interactions remain biologically relevant e.g. a virus–host protein–protein interaction. An interaction also stores a text description, cellular place of interaction, experimental conditions used to observe binding, a comment on evolutionarily conserved biological sequence, binding sites on A and B and how they are connected, chemical action including kinetic and thermodynamic data and chemical state of the molecules involved. The specification can store 3D structure level of detail in object representations, binding site and chemical action descriptions.

Data is entered into BIND either by manual or automatic methods. Expert curators on the BIND team are entering high quality records on a continuing basis. Users are encouraged to enter records into the database via the web-based system, or to contact the BIND staff if they have large data sets they want to process. A simple submission involves entering contact information (which only needs to be done the first time you submit to BIND), the PubMed identifier and two interacting molecules (which can easily be identified by their gi identifiers). Every record that is entered in this way will be validated by BIND indexers and by at least one other expert before it is made available in any public data release.

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