BRENDA in 2015: exciting developments in its 25th year of existence

By Antje Chang, I. Schomburg, S. Placzek, Lisa Jeske, Marcus Ulbrich, Mei Xiao, C. Sensen, Dietmar Schomburg. 2014

198 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology, Computational Biology & Bioinformatics

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Citations in the corpus

Predicting multicellular function through multi-layer tissue networks (2017, methodology): “We retrieved the mapping of tissues in the Human Protein Reference Database (HPRD) (Prasad et al. , 2009) to tissues in the BRENDA Tissue Ontology (Chang et al. , 2014) from Greene et al. (2015).”
BRENDA, the ELIXIR core data resource in 2021: new developments and updates (2020, methodology): “Since 2015 the human anatomy atlas CAVEman, based on the ‘Terminologia Anatomica’, is linked to BRENDA to connect human enzymes to the detailed ontology of body parts, organs, and tissues (8,9).”
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB (2015, background): “For enzymes, information is shown on the reaction catalysed and other relevant comments on function or biological availability of the particular enzyme obtained from enzyme resources such as IntEnz (45), Brenda (46) and Expasy (47).”
BRENDA in 2019: a European ELIXIR core data resource (2018, background): “Additionally, the human anatomy atlas CAVEman (6,7) is linked to the BTO terms providing a connection between anatomical and functional enzyme data.”