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Rhea

Explore Rhea, a comprehensive manually annotated database of biochemical reactions, providing stable identifiers, stoichiometry validation, and reaction decompositions. Benefit from cross-references, bibliographic citations, and search functionalities. Comparison with similar databases highlights Rhea's consistency, directionality, and stoichiometry checks. Access compounds with unique names normalized to pH 7.3. Rhea offers simple and advanced search options, downloadable formats, web services, and insightful exercises. Learn about the history and evolution of BRENDA, the prominent enzyme database.

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Rhea

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  1. Rhea Annotated reactions database

  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

  3. 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 Rhea

  4. www.ebi.ac.uk/rhea Rhea

  5. What does Rhea provide • Stable reaction identifiers and directionality (or lack of it). • Reaction participants linked to ChEBI 5 02.02.09 Rhea

  6. What does Rhea provide (continued) • Validation of stoichiometry (mass and charge balance) • Families of reactions 6 02.02.09 Rhea

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

  8. What does Rhea provide (continued) • Cross references. • Bibliographic citations. Rhea 02.02.09

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

  10. 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 Rhea

  11. Simple search • By compound name: • urea • Caffe* • a?e?o* • By compound identifier: • CHEBI:17015 11 Rhea

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

  13. Advanced Search - Chemical Search type Search on formula and range searches Rhea selected 02.02.09 Rhea

  14. Advanced Search Example 02.02.09 Rhea

  15. Advanced Search Example (continued) 02.02.09 Rhea

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

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

  18. Exercises! http://www.ebi.ac.uk/rhea Rhea

  19. 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 1st Edition 1990-1997 2nd 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

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

  21. Biochemical and molecular properties of enzymes stored in BRENDA:

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