IntEnz - The Enzyme Database in Oracle

Astrid Fleischmann1, Michael Darsow, Kirill Degtyarenko and Rolf Apweiler




EMBL Outstation, European Bioinformatics Institute,
Hinxton, Cambridge, UK
1Phone: +44 (0)1223 494 444
Fax: +44 (0)1223 494 468
E-mail: Astrid.Fleischmann@ebi.ac.uk
http://www.ebi.ac.uk/enzyme





IntEnz is the name for the Integrated relational Enzyme database. IntEnz is supported by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) and will contain enzyme data approved by the Nomenclature Committee.

The relational database (IntEnz) implemented and supported by the EBI will be the master copy of the Enzyme database. The goal is to create a single relational database containing enzyme data from three different sources:

  1. The Trinity College Dublin (TCD) maintains on behalf of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) the Enzyme Classification list and is involved in many other aspects of biochemical nomenclature.

  2. The Swiss Institute of Bioinformatics (SIB) produces an Enzyme Nomenclature database (ENZYME).

  3. The University of Cologne produces an enzyme function database (BRENDA), which contains a large amount of information on substrates, products, and inhibitors.

The EBI has already implemented a relational database version of the ENZYME database of the SIB. The relational database IntEnz will be further populated by the corresponding data from the Enzyme Classification list of TCD and from BRENDA. Resolving any discrepancies between the equivalent data fields from these three data sets is the first step towards a controlled vocabulary for biochemical terminology. These common data comprise the EC number, recommended name of an enzyme, systematic name of an enzyme, alternative name(s) of an enzyme, catalytic activity, cofactors, comments, and references. The EBI is also developing tools to maintain the database and allow propagation of new and updated biochemical terminology, which has been integrated into the database, to the other partners. The representation of enzyme data will be done in a number of different ways, including a JCBN/IC-IUBMB authorized view of the data.

The EBI also set up Internet services which initially facilitate text-based searches against the relational databases such as the protein sequence databases (SWISS-PROT, TrEMBL, TrEMBLnew), the protein family signature database (InterPro), Gene Ontology (GO), IntEnz and BRENDA.