|
 | | Loading... |
About Rhea
1. Introduction
The ability to describe biochemical reactions precisely constitutes a very
important task as it is the foundation for accurate modelling of metabolic
networks and calculating metabolite fluxes in biological systems. Several
current efforts, such as KEGG and MetaCyc,
use the Enzyme
Commission (EC) list
as a basis to create enzymatically catalysed reactions, as the EC numbering
system provides both a formal description of the enzymes and a categorisation
of the enzymatic reaction taking place. Unfortunately, none of the existing
databases (the EC list included) can provide a set of completely balanced
reactions, nor do they provide a completely consistent use of compound names.
To improve the current situation we have constructed a new reaction database
(Rhea). 2. What is Rhea?
Rhea is a reaction database, where all reaction participants (reactants and
products) are linked to the ChEBI database (Chemical Entities of Biological
Interest) which provides detailed information about structure, formula and
charge. Rhea provides built-in validations that ensure both elemental and
charge balance of the reactions. We have populated the database with the
reactions found in the EC list (and in the
IntEnz and
ENZYME databases),
extending it with additional known reactions of biological interest.
While the main focus of Rhea is enzyme-catalysed reactions,
other biochemical reactions (including those that are often termed "spontaneous")
also are included.
Rhea is a manually annotated resource and it provides:
- Stable reaction identifiers for each of its reactions. These identifiers
are independent of EC numbers but are linked to EC numbers via
cross-references.
- Directionality information if the physiological direction of the reaction
is known.
- The possibility to link several reactions together to form complex
reactions. This feature can also be used to split reactions into partial
reactions.
- Extensive cross-references to other resources including enzyme-catalysed
and other metabolic reactions, such as the EC list
(in IntEnz),
KEGG,
MetaCyc and
UniPathway.
- Chemical substructure and similarity searches on compounds in Rhea,
thereby allowing reactions to be found where similar compounds are
involved.
The database is extensively cross-referenced. Reactions are currently
linked to the
EC list,
KEGG and
MetaCyc, and the reactions
will be used in the
IntEnz database
and in all relevant
UniProtKB entries.
Furthermore, the reactions will also be used in the
UniPathway database to generate pathways and metabolic
networks. 4. Availability
Rhea is available via this public web interface. In addition,
all the data isdownloadable in its
entirety, and is free to anyone without restriction. 5. About the name
In classical Greek mythology, Rhea
(greek Ρέα; /ˈriːə/) was the daughter of Uranus and Gaia, and was known as the
mother of gods. Her name is often linked to the Greek word ρείν ("flow") but has no
relation to the word "reaction".
Rhea is the name of a genus of flightless birds, also known
as ñandú.
Rhea is also the name of the second-largest moon of
Saturn, which contains up to 75% water and may have a tenuous ring system.
The image of Rhea (moon) is used in Rhea (database) logo. 6. How to cite Rhea
Rafael Alcántara, Kristian B. Axelsen, Anne Morgat, Eugeni Belda, Elisabeth
Coudert, Alan Bridge, Hong Cao, Paula de Matos, Marcus Ennis, Steve Turner,
Gareth Owen, Lydie Bougueleret, Ioannis Xenarios, Christoph Steinbeck
Rhea - a manually curated resource of biochemical reactions
|