IntEnz is the name for the Integrated relational Enzyme database. IntEnz will contain enzyme data approved by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB).
For many years, Amos Bairoch has been supporting the Enzyme Nomenclature database, appropriately called ENZYME. Indeed, this was the only electronic version of The Enzyme Nomenclature. For the big part of the bioinformatics communtity, ENZYME is the Enzyme Nomenclature. An obvious example is its use for SWISS-PROT annotation. However, in spite of containing the data from The Enzyme Nomenclature, it was never considered an official publication on The Enzyme Nomenclature (as opposed to, say, Enzyme Nomenclature 1992, Academic Press, San Diego). ENZYME exists as a plain ASCII text file.
The Web Version of Enzyme Nomenclature has been prepared by Gerry Moss and includes the complete contents of Enzyme Nomenclature 1992 plus subsequent supplements and other changes. It is official and easy to navigate. However it is not a true database but a set of manually edited HTML pages.
During their course of evolution, ENZYME, Enzyme Nomenclature and other databases containing enzyme-related information accumulated a number of discrepancies in the data that are meant to be identical. These discrepancies could be anything e.g. typos, corrections, new data or their absence. With more new data, it is becoming difficult to keep these sources in sync.
The goal of the IntEnz project is to have a relational database that integrates all of the Enzyme Nomenclature.
After the BioBabel grant, no active funding is available to actively develop IntEnz. None of the annotators funded by new Felics grant will be based at the EBI.
SIB (enzyme annotation).
Since most of the data in IntEnz will have "official" status, the mechanism of approval by NC-IUBMB had to be implemented. The data will enter IntEnz in one of two ways:
Since IntEnz is one of the sources of terminology for ChEBI database, it was logical to link all the compound terms in reaction and cofactor fields of IntEnz to corresponding ChEBI entries.
Initially, the reaction field in an IntEnz entry was a free text. We aimed to improve quality of reaction data in IntEnz and provide other databases with the new means of annotation by
The main product of this project is a relational database, IntEnz,
which can be queried via the web interface.
The updated figures can be found in the
Currently, we don't provide a downloadable database dump, which would be an Oracle dump only usable by Oracle installations.
The contents of the relational database can be browsed in form of HTML files in the IntEnz website, which show not only the IntEnz (integrated data) view, but also the NC-IUBMB and SIB views.
The contents of the relational database is exported every night in form of ASCII file (enzyme_intenz.dat). It is essentially identical to the enzyme.dat flat file prepared by SIB (found at ftp://ftp.expasy.org/databases/enzyme/) which is used e.g. for UniProt anotation. In fact, the enzyme_intenz.dat file is used by SIB curators as a basis for their work to produce enzyme.dat. That way, enzyme data is curated just once using the IntEnz curator tool.
For compatibility with a broadly used standard, IntEnz is also exported as a BioPAX file.
Most of IntEnz annotation is done from outside of the EBI with the help of the IntEnz Curator Tool.