EBI is an Outstation of the European Molecular Biology Laboratory. Rhea Annotated reactions database...
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EBI is an Outstation of the European Molecular Biology Laboratory.
Rhea
Annotated reactions database
April 21, 2023
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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....
Rhea2 April 21, 2023
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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 April 21, 2023
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www.ebi.ac.uk/rhea
Rhea4 April 21, 2023
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Rhea02.02.095
What does Rhea provide
• Stable reaction identifiers and directionality (or lack of it).
• Reaction participants linked to ChEBI
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Rhea02.02.096
What does Rhea provide (continued)
• Validation of stoichiometry (mass and charge balance)
• Families of reactions
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What does Rhea provide (continued)
• Decompositions of reactions in elementary processes ordered in time (steps) or not (coupled).
Rhea
02.02.097 April 21, 2023
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What does Rhea provide (continued)
• Cross references.
• Bibliographic citations.
Rhea
02.02.098 April 21, 2023
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Rhea9
Rhea compared to similar reaction DBs
• Consistency in the use of compounds and their nomenclature.
• Directionality.
• Stoichiometry check.
• Independence from spatial location.
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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 April 21, 2023
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Rhea11
Simple search
• By compound identifier:CHEBI:17015
• By compound name:ureaCaffe*a?e?o*
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Rhea
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 ).
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Rhea17
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.
April 21, 2023
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Rhea
Exercises!
http://www.ebi.ac.uk/rhea
April 21, 2023
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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
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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
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22
Biochemical and molecular properties of enzymes stored in BRENDA: