BIND - a data specification for storing and describing biomolecular interactions, molecular complexes and pathways

Motivation: Proteomics is gearing up towards high-throughput methods for id entifying and characterizing all of the proteins, protein domains and prote in interactions in a cell and will eventually create more recorded biologic al information than Human Genome Project. Each protein expressed in a cell can interact with various other proteins and molecules in the course of its function. A standard data specification is required that can describe and store this information in all its detail and allow efficient cross-platform transfer of data. A complete specification must be the basis for any datab ase or tool for managing and analysing this information. Results: We have defined a complete data specification in ASN.1 that can de scribe information about biomolecular interactions, complexes and pathways. Our group is using this data specification in our database, the Biomolecul ar Interaction Network Database (BIND). An interaction record is based on t he interaction between two objects. An object can be a protein, DNA, RNA, l igand, molecular or an interaction. Interaction description encompasses cel lular location experimental conditions used to observe the interaction, con served sequence, molecular location, chemical action, kinetics, thermodynam ics, and chemical state. Molecular complexes are defined as collections of more than two interactions that form a complex, with extra descriptive info rmation such as complex topology. Pathways are defined as collections of mo re than two interactions that forma pathway, with additional descriptive in formation such as cell cycle stage. A request for proposal of a human reada ble flat-file format that mirrors the BIND data specification is also tende red for interested parties. Availability: The ASN.1 data specification for biomolecular interaction, mo lecular complex and pathway data is available at ftp://bioinfo.mshri.on.ca/ pub/BIND/Spec/bind.asn. An interactive browser for this document is availab le through our homepage at http://bioinfo.mshri.on.ca/BIND/asn-browser/. Contact: hogue @ mshri.on.ca.