Rhea

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General Information

Rhea is a comprehensive and non-redundant resource of expert-curated biochemical reactions designed for the functional annotation of enzymes and the description of metabolic networks. Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature list as well as additional reactions, including spontaneously occurring reactions, using entities from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules.

Homepage http://www.rhea-db.org

Developed in European Union , Switzerland

Created in 2009

Taxonomic range

Scope and data types

In the following recommendations:

How to cite this record FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: Feb. 22, 2018, 2:44 p.m.; Last accessed: Sep 21 2018 8:29 a.m.

This record is maintained by amorgat

Record updated: March 20, 2017, 4:56 p.m. by amorgat.

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Edits to 'https://fairsharing.org/FAIRsharing.pn1sr5' by 'amorgat' at 08:46, 02 Dec 2016 (approved):

	'description' has been modified:
		Before: Rhea is a comprehensive and non-redundant resource of biochemical reactions described using species from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. Rhea has been designed for the functional annotation of enzymes and the description, analysis and reconciliation of genome-scale metabolic networks.
		After: Rhea is a comprehensive and non-redundant resource of expert-curated biochemical reactions designed for the functional annotation of enzymes and the description of metabolic networks. Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature list as well as additional reactions, including spontaneously occurring reactions, using entities from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules.  Publication List has changed:  Previous values: Updates in Rhea--a manually curated resource of biochemical reactions. Rhea--a manually curated resource of biochemical reactions. Updates in rhea-an expert curated resource of biochemical reactions. New values:  Updates in Rhea--a manually curated resource of biochemical reactions. Rhea--a manually curated resource of biochemical reactions. Added Rhea to policy F1000Research Data Policy.

Edits to 'https://fairsharing.org/FAIRsharing.pn1sr5' by 'amorgat' at 12:29, 30 Nov 2016 (approved):

	'contactEmail' has been modified:
		Before: anne.morgat@isb-sib.ch
		After: anne.morgat@sib.swiss Domain list has changed:  Previous values: Biochemistry|process|http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Scientific-Discipline.owl#nlx_inv_100610 Chemical entity|material|http://purl.obolibrary.org/obo/CHEBI_24431 Enzymatic reaction|process|http://purl.obolibrary.org/obo/MI_0414 Life Science|domain| Manual curation|x| Reaction|| Small molecule|material| New values:  Biochemistry|process|http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Scientific-Discipline.owl#nlx_inv_100610 Enzymatic reaction|process|http://purl.obolibrary.org/obo/MI_0414 Reaction|| Chemical entity|material|http://purl.obolibrary.org/obo/CHEBI_24431 Small molecule|material| Life Science|domain| Manual curation|x| Countries have changed:  Previous values: European Union Switzerland New values:  Switzerland European Union Publication List has changed:  Previous values: Updates in Rhea--a manually curated resource of biochemical reactions. Rhea--a manually curated resource of biochemical reactions. New values:  Updates in Rhea--a manually curated resource of biochemical reactions. Rhea--a manually curated resource of biochemical reactions. Updates in rhea-an expert curated resource of biochemical reactions. Organisations have changed:  Previous values: European Bioinformatics Institute (EMBL-EBI)|Wellcome Trust Genome Campus|Hinxton|Cambridge|UK European Commission FP7 SIB|Swiss Institute of Bioinformatics Swiss Federal Government (SERI) SystemsX.ch New values:  SIB|Swiss Institute of Bioinformatics European Bioinformatics Institute (EMBL-EBI)|Wellcome Trust Genome Campus|Hinxton|Cambridge|UK Swiss Federal Government (SERI) SystemsX.ch Grants have changed:  Previous values: 222886-2 New values:  Added Rhea to policy F1000Research Data Policy.

Edits to 'https://fairsharing.org/FAIRsharing.pn1sr5' by 'The FAIRsharing Team' at 14:14, 08 Sep 2016 (approved):

	'name' has been modified:
		Before: Rhea: an expert curated resource of biochemical reactions
		After: Rhea

Edits to 'https://fairsharing.org/FAIRsharing.pn1sr5' by 'The FAIRsharing Team' at 17:39, 02 Sep 2016 (approved):

	'contactName' has been modified:
		Before:
			Anne MORGAT
		After:
			Anne Morgat
			Data processes have changed: 
			Previous values:
			FTP download
			monthly release
			manual curation
			user request
			web interface
			web service
			New values: 
			FTP download
			monthly release
			manual curation
			user request
			advanced search
			submit
			browse
		Added:
		Removed:

In Collections

Data Citation Implementation

ELIXIR node contributed resources

Chemistry

Support

General

contact form	http://www.rhea-db.org/feedback
online documentation	http://www.rhea-db.org/documentation

Additional Information

Contact	Anne Morgat
Identifiers.org	MIR:00000082

Tools

RxnSim	https://cran.r-project.org/web/packages/RxnSim/index.html	1.0.1
Metabolic Tinker	http://osslab.lifesci.warwick.ac.uk/tinker.aspx
ChemAxon	https://www.chemaxon.com/

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Creative Commons Attribution 4.0 International (CC BY 4.0)

Data Release

monthly release

http://www.rhea-db.org/download

Data Curation

manual curation	No link recorded
user request	http://www.rhea-db.org/submit
submit	http://www.rhea-db.org/submit

Data Access

FTP download	ftp://ftp.ebi.ac.uk/pub/databases/rhea
advanced search	http://www.rhea-db.org/advancedsearch
browse	http://www.rhea-db.org/searchresults?q=chebi*

REST Web Services

Rhea webservice

http://www.rhea-db.org/rest/1.0/ws/reaction?q=caffeine

Publications

Updates in Rhea--a manually curated resource of biochemical reactions.

Morgat A, Axelsen KB, Lombardot T, Alcántara R, Aimo L, Zerara M, Niknejad A, Belda E, Hyka-Nouspikel N, Coudert E, Redaschi N, Bougueleret L, Steinbeck C, Xenarios I, Bridge A.
Nucleic Acids Res. 2014

View Paper (PubMed) View Publication

Rhea--a manually curated resource of biochemical reactions.

Alcantara R,Axelsen KB,Morgat A,Belda E,Coudert E,Bridge A,Cao H,de Matos P,Ennis M,Turner S,Owen G,Bougueleret L,Xenarios I,Steinbeck C
Nucleic Acids Res. 2011

View Paper (PubMed) View Publication

Updates in Rhea - an expert curated resource of biochemical reactions.

Morgat A, Lombardot T, Axelsen KB, Aimo L, Niknejad A, Hyka-Nouspikel N, Coudert E, Pozzato M, Pagni M, Moretti S, Rosanoff S, Onwubiko J, Bougueleret L, Xenarios I, Redaschi N, Bridge A.
Nucleic Acids Res. 2017

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Models and Formats

Related Databases

Implementing Policies

Wellcome Open Research Data Guidelines

Credit

Record Maintainer

This record is maintained by amorgat

Funds

Swiss Federal Government (SERI)
SystemsX.ch (Government body)

Maintains

Swiss Institute of Bioinformatics (SIB), Switzerland (Research institute)

Undefined

European Commission under FP7 Grant Agreement (Government body)

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