BRENDA (BRaunschweig ENzyme Database) is the world’s largest information system for biochemical, molecular biological and functional enzyme data. BRENDA contains information about all sufficiently characterized and by the IUBMB classified enzymes. Over 3 million enzyme-specific functional datasets have been extracted and structured by experts in biochemistry, biology and chemistry from over 130,000 scientific publications. These datasets include information on catalyzed reactions, the specification of the enzymes, their occurrence, stability, inhibitors, substrates, products, kinetic information, applications, etc. In addition, BRENDA integrates data from numerous other databases as well as from text-mining methods and from bioinformatics-application calculated data. Each entry is assigned to a publication and an organism. BRENDA is freely accessible to all academic institutions. More than 80 000 users access the BRENDA website every month, mainly from North America, Asia and Europe.
BRENDA Enzyme Information System for Metabolome Research, Enzyme Technology and Systems Biology Motivation.
The BRENDA database is the most comprehensive enzyme information system in the field of biochemical research. The goal of the project is the continuous integration of new enzyme-specific data and detailed information on the occurrence and functions of enzymes. The user interface integrates simple and highly complex query methods, which take into account the complexity of the stored data (numerical data, text data, images, domains, ontologies, and hierarchies) and allows a wide range of applications in the different life sciences.
Challenges & Highlights
The main challenge is to manually and automatically extract the unstructured information which is available in the constantly and rapidly increasing flood of scientific literature. These pieces of information then must be linked to other data - calculated or available in repositories - to give a specific idea of the many thousands of enzymes and to make this information efficiently accessible to the user through efficient query systems and visual processing. Each entry in BRENDA is linked to a source reference (e.g. citation of a scientific publication). The enzyme data can be assigned to the original organism, organs, tissues, plant parts, cell cultures, cell compartments or protein sequences. 3 million hand annotated datasets are exceeded many times over by integrated text mining and other data. Artificial intelligence methods are used to evaluate the relevance of publications on diseases and their relation to enzyme functions and malfunctions (Support Vector Machines). Furthermore, BRENDA contains structures and functional data on more than ~190,000 ligands that interact with enzymes as substrates/products, cofactors, inhibitors, etc. These can be searched and visualized using substructure search algorithms. The development work is complemented by the participation in international committees, such as the IUBMB Enzyme Task Force and the IUBMB Biochemical Nomenclature Committee. The BRENDA group is at the forefront of international activities in ontology development and data semantics due to the development of the BRENDA Tissue Ontology (BTO), an ontology of organs, tissues and cell cultures.
Potential Applications & Future Plans
BRENDA is one of the most important and widely used enzyme information systems in the life sciences worldwide. The extensive data is used in basic research in biochemistry, molecular biology and systems biology as well as in medical research. It plays an important role in industrial research of drug discovery and biotechnology. Intensive interaction with users and discussions at scientific congresses ensure that BRENDA remains one of the most important information systems worldwide, both in terms of the scientific needs of its users and the latest scientific developments.