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

2. 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

3. 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. 3 17 December 2015

4. www.ebi.ac.uk/rhea Rhea 4 17 December 2015

5. Rhea02.02.095 What does Rhea provide Stable reaction identifiers and directionality (or lack of it). Reaction participants linked to ChEBI 5 17 December 2015

6. Rhea02.02.096 What does Rhea provide (continued) Validation of stoichiometry (mass and charge balance) Families of reactions 6 17 December 2015

7. What does Rhea provide (continued) Decompositions of reactions in elementary processes ordered in time (steps) or not (coupled). Rhea 02.02.09 7 17 December 2015

8. What does Rhea provide (continued) Cross references. Bibliographic citations. Rhea 02.02.09 8 17 December 2015

9. Rhea9 Rhea compared to similar reaction DBs Consistency in the use of compounds and their nomenclature. Directionality. Stoichiometry check. Independence from spatial location. 9 17 December 2015

10. 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). 10 17 December 2015

11. Rhea11 Simple search By compound identifier:  CHEBI:17015 By compound name:  urea  Caffe*  a?e?o* 11 17 December 2015

12. Advanced Search - Text Rhea Select category Filter by attribute Menu Filter by cross- referenced database 12 17 December 2015

13. Advanced Search - Chemical Rhea02.02.09 Search type Search on formula and range searches Rhea selected 13 17 December 2015

14. Advanced Search Example Rhea02.02.09 14 17 December 2015

15. Advanced Search Example (continued) Rhea02.02.09 15 17 December 2015

16. Rhea Downloads BioPAX format (http://www.biopax.org). RXN format (http://www.mdl.com).http://www.mdl.com RD format (http://www.mdl.com).http://www.mdl.com Compounds: RD, SDF formats (http://www.mdl.com ). 16 17 December 2015

17. Rhea17 Web services http://www.ebi.ac.uk/rhea/rest/1.0/ Simple text search RXN format (http://www.mdl.com).http://www.mdl.com BioPAX level 2 format (http://www.biopax.org). CMLReact format. 17 December 2015

18. 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) http://www.ebi.ac.uk/rhea ftp://ftp.ebi.ac.uk/pub/databases/rhea http://sourceforge.net/projects/rhea-ebi rhea-ebi-help@lists.sourceforge.net 18 17 December 2015

19. Rhea Exercises! http://www.ebi.ac.uk/rhea 17 December 2015

20. 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 1990-1997 2 nd Edition 2000-2009 (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. 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. 22 Biochemical and molecular properties of enzymes stored in BRENDA:

23. 23 Feedback: please complete the short survey at