EBI is an Outstation of the European Molecular Biology Laboratory. Rhea Annotated reactions database 17 December 2015

Motivation for decomposed reactions The reactions provided by the NC-IUBMB are free-text... Can result in duplicate reactions for example.... acetic acid + ATP + CoA acetyl-CoA + AMP is the same as acetic acid + CoA + ATP acetyl-CoA + AMP But unless you tell a computer that it will just interpret two different strings.... Rhea 2 17 December 2015

Rhea3 What is Rhea A manually annotated database of reactions. Initially populated with reactions from the EC nomenclature (IntEnz/ENZYME) databases. Also contains non-enzymatic (spontaneous) reactions of biological interest December 2015

Rhea 4 17 December 2015

Rhea What does Rhea provide Stable reaction identifiers and directionality (or lack of it). Reaction participants linked to ChEBI 5 17 December 2015

Rhea What does Rhea provide (continued) Validation of stoichiometry (mass and charge balance) Families of reactions 6 17 December 2015

What does Rhea provide (continued) Decompositions of reactions in elementary processes ordered in time (steps) or not (coupled). Rhea December 2015

What does Rhea provide (continued) Cross references. Bibliographic citations. Rhea December 2015

Rhea9 Rhea compared to similar reaction DBs Consistency in the use of compounds and their nomenclature. Directionality. Stoichiometry check. Independence from spatial location December 2015

Rhea10 Compounds in Rhea Unique name (SOURCE='UniProt' in ChEBI) → 'CoA'/'CoA-SH'/'Coenzyme A' problem solved. Normalized to pH 7.3. Updated with any changes in ChEBI (name, formula, merging of ChEBI ID) December 2015

Rhea11 Simple search By compound identifier:  CHEBI:17015 By compound name:  urea  Caffe*  a?e?o* December 2015

Advanced Search - Text Rhea Select category Filter by attribute Menu Filter by cross- referenced database December 2015

Advanced Search - Chemical Rhea Search type Search on formula and range searches Rhea selected December 2015

Advanced Search Example Rhea December 2015

Advanced Search Example (continued) Rhea December 2015

Rhea Downloads BioPAX format ( RXN format ( RD format ( Compounds: RD, SDF formats ( ) December 2015

Rhea17 Web services Simple text search RXN format ( BioPAX level 2 format ( CMLReact format. 17 December 2015

Rhea team and resources Rafael Alcántara (Developer, EBI) Kristian Axelsen (Curator, SIB) Anne Morgat (Curator, SIB) Mohamed Zerara (Developer, SIB) Alan Bridge (Coordinator, SIB) Paula de Matos (Coordinator, EBI) Christoph Steinbeck (Team leader, EBI) ftp://ftp.ebi.ac.uk/pub/databases/rhea December 2015

Rhea Exercises! 17 December 2015

A short history of BRENDA BRaunschweig ENzyme DAtabase 1987 project started at German National Research Centre for Biotechnology in Braunschweig originally published as a series of books 1 st Edition nd Edition (45 Volumes) available in print and pdf-format 1996 BRENDA and Dietmar Schomburg moved to University of Cologne here BRENDA was further curated and transformed into a publicly available database 2007 BRENDA moved back to Braunschweig (Technische Universität) continuous curation, technical improvement and further development

21 ● Enzymes ● Classification and Nomenclature ● Reaction & Specificity ● Enzyme Structure ● Isolation & Preparation ● Stability ● Kinetic data ● Links & Literature References ● Metabolites/Ligands ● Nomenclature ● Structure ● Role ● Occurrence/concentration Most comprehensive information system on ● Enzymes > 3,2 million enzyme-specific data > 100,000 literature references ~ 5,000 EC numbers Data categories

22 Biochemical and molecular properties of enzymes stored in BRENDA:

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