EBI is an Outstation of the European Molecular Biology Laboratory.

Rhea

Annotated reactions database

April 21, 2023

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

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

www.ebi.ac.uk/rhea

Rhea4 April 21, 2023

Rhea02.02.095

What does Rhea provide

• Stable reaction identifiers and directionality (or lack of it).

• Reaction participants linked to ChEBI

5 April 21, 2023

Rhea02.02.096

What does Rhea provide (continued)

• Validation of stoichiometry (mass and charge balance)

• Families of reactions

6 April 21, 2023

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

What does Rhea provide (continued)

• Cross references.

• Bibliographic citations.

Rhea

02.02.098 April 21, 2023

Rhea9

Rhea compared to similar reaction DBs

• Consistency in the use of compounds and their nomenclature.

• Directionality.

• Stoichiometry check.

• Independence from spatial location.

9 April 21, 2023

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

Rhea11

Simple search

• By compound identifier:CHEBI:17015

• By compound name:ureaCaffe*a?e?o*

11 April 21, 2023

Advanced Search - Text

Rhea

Select

category

Filter by

attribute

Menu

Filter by cross-

referenced database

12 April 21, 2023

Advanced Search - Chemical

Rhea02.02.09

Search

type

Search on

formula and

range searches

Rhea

selected

13 April 21, 2023

Advanced Search Example

Rhea02.02.0914 April 21, 2023

Advanced Search Example (continued)

Rhea02.02.0915 April 21, 2023

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 ).

16 April 21, 2023

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

Rhea

Exercises!

http://www.ebi.ac.uk/rhea

April 21, 2023

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

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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Biochemical and molecular properties of enzymes stored in BRENDA: