Standardization in enzymology—Data integration in the world׳s enzyme information system BRENDA

In the modern life sciences literature search is mainly done electronically and huge datasets obtained by the use of diverse experimental methods have to be integrated to perform an in depth analysis of biological systems. This means that standardization is absolutely essential to allow the identification of all relevant data, their comparison and finally their integration. The main areas in enzymology where standardisation would be required but is not achieved yet are (i) use of standard nomenclature for enzymes and ligands, and (ii) the full registration and standardisation of experimental condition for function analysis. The accepted or recommended names as defined by the IUBMB biological nomenclature committee are both descriptive and unambiguous, but unfortunately not used in all papers. In addition to the enzyme names unambiguousness is needed for the ligand names, the enzyme׳s origin as given by the organism name, a tissue name and the description of the subcellular localisation. A comparison of enzyme functional parameters is only possible when the experimental conditions are fully characterised and ideally standardized.The BRENDA enzyme database and its addenda (AMENDA, FRENDA, DRENDA) as the world׳s main information system for enzyme function and other properties makes use of standards as far as possible, but also provides non-standard names and other non-standard data, relating them to the appropriate standard. For example the enzyme nomenclature part of BRENDA includes about 82,000 synonyms for the classified enzymes, linking them to the standard accepted name. The definition of the biological enzyme sources are based on ontologies and controlled vocabularies. Kinetic data are reported together with the experimental conditions where available from the literature. For the enzyme ligands chemical structures allow an unambiguous identification.