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Rhea

Rhea. Annotated reactions database. 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

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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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