Abstract
The BRENDA enzyme information system (http://www.brenda-enzymes.org/) has developed into an elaborate system of enzyme and enzyme-ligand information obtained from different sources, combined with flexible query systems and evaluation tools. The information is obtained by manual extraction from primary literature, text and data mining, data integration, and prediction algorithms. Approximately 300 million data include enzyme function and molecular data from more than 30 000 organisms. The manually derived core contains 3 million data from 77 000 enzymes annotated from 135 000 literature references. Each entry is connected to the literature reference and the source organism. They are complemented by information on occurrence, enzyme/disease relationships from text mining, sequences and 3D structures from other databases, and predicted enzyme location and genome annotation. Functional and structural data of more than 190 000 enzyme ligands are stored in BRENDA. New features improving the functionality and analysis tools were implemented. The human anatomy atlas CAVEman is linked to the BRENDA Tissue Ontology terms providing a connection between anatomical and functional enzyme data. Word Maps for enzymes obtained from PubMed abstracts highlight application and scientific relevance of enzymes. The EnzymeDetector genome annotation tool and the reaction database BKM-react including reactions from BRENDA, KEGG and MetaCyc were improved. The website was redesigned providing new query options.
Highlights
BRENDA (BRaunschweig ENzyme DAtabase; http:// www.brenda-enzymes.org/), the major public information system for functional and molecular properties of enzymes, celebrated its 25th anniversary in 2013. It was started as a series of books [Handbook of Enzymes, [1]] to provide a substantial enzyme repository, based on the Enzyme Commission (EC) classification system of the IUBMB [International Union of Biochemistry and Molecular Biology, [2]]
Since 1998 BRENDA has been available via the Internet with a first query system
With the fast growing number of data and knowledge in the ‘OMICS’ area, the continuous integration of new data and new developments in BRENDA has to meet the expectations as an enzyme and enzyme function data resource for systems biology, biotechnology, medical research and related fields
Summary
BRENDA (BRaunschweig ENzyme DAtabase; http:// www.brenda-enzymes.org/), the major public information system for functional and molecular properties of enzymes, celebrated its 25th anniversary in 2013. BRENDA contains information on all classified enzymes of organisms of all taxonomic groups. BRENDA includes large amounts of information on the occurrence of enzymes in organisms, their cellular localization, their involvement in human diseases, their active centers and interfaces, as well as additional kinetic data, resulting from text mining and analysis methods and bioinformatics approaches [3,4]. Integrated are ‘Word Maps’ that provide graphical information on terms and perceptions associated with specific enzymes.
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