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

All

Knowledge Domains BETA

Subjects BETA

In the following recommendations:

How to cite this record FAIRsharing.org: Rhea; Rhea; DOI: https://doi.org/10.25504/FAIRsharing.pn1sr5; Last edited: Jan. 17, 2019, 12:55 p.m.; Last accessed: Feb 16 2019 9:08 p.m.

Publication for citation 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; 10.1093/nar/gkw990;

This record is maintained by amorgat

Record updated: Jan. 17, 2019, 12:55 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.pn1sr5' by 'The FAIRsharing Team' at 12:55, 17 Jan 2019 (approved):

	'organizations' has been modified:
		Before:
			Swiss Federal Government (SERI)|https://www.sbfi.admin.ch/sbfi/en/home.html|Funds
			SystemsX.ch|http://www.systemsx.ch/|Funds
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		After:
			Swiss Federal Government (SERI)|https://www.sbfi.admin.ch/sbfi/en/home.html|Funds
			SystemsX.ch|http://www.systemsx.ch/|Funds
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Funds
		Added:
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Funds
		Removed:
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined

Edits to 'https://fairsharing.org/FAIRsharing.pn1sr5' by 'The FAIRsharing Team' at 12:55, 17 Jan 2019 (approved):

	'organizations' has been modified:
		Before:
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined
			Swiss Federal Government (SERI)|https://www.sbfi.admin.ch/sbfi/en/home.html|Funds
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			SystemsX.ch|http://www.systemsx.ch/|Funds
		After:
			Swiss Federal Government (SERI)|https://www.sbfi.admin.ch/sbfi/en/home.html|Funds
			SystemsX.ch|http://www.systemsx.ch/|Funds
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Added:
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Removed:

	'related_databases' has been modified:
		Before:
			Mechanism, Annotation and Classification in Enzymes
			MetaCyc
			MetaboLights
			Reactome - a curated knowledgebase of biological pathways
			UniPathway
			UniProt Knowledgebase
			Kyoto Encyclopedia of Genes and Genomes
			SwissLipids
			MetaNetX
		After:
			Mechanism, Annotation and Classification in Enzymes
			MetaCyc
			MetaboLights
			Integrated relational Enzyme database
			Reactome - a curated knowledgebase of biological pathways
			UniPathway
			UniProt Knowledgebase
			Kyoto Encyclopedia of Genes and Genomes
			SwissLipids
			MetaNetX
			Enzyme nomenclature database
		Added:
			Integrated relational Enzyme database
			Enzyme nomenclature database
		Removed:

	'supportLinks' has been modified:
		Before:
			contact form|http://www.rhea-db.org/feedback
			online documentation|http://www.rhea-db.org/documentation
		After:
			contact form|http://www.rhea-db.org/feedback
			online documentation|http://www.rhea-db.org/documentation
			online documentation|https://www.rhea-db.org/statistics
		Added:
			online documentation|https://www.rhea-db.org/statistics
		Removed:

	'dataProcesses' has been modified:
		Before:
			FTP download
			monthly release
			manual curation
			user request
			advanced search
			submit
			browse
		After:
			FTP download
			Download Data
			manual curation
			Data Submission
			Advanced search
			Browse
		Added:
			Download Data
			Data Submission
			Advanced search
			Browse
		Removed:
			monthly release
			user request
			advanced search
			submit
			browse

	'accessPoints' has been modified:
		Before:
			REST|http://www.rhea-db.org/rest/1.0/ws/reaction?q=caffeine|Rhea webservice
		After:
			REST|https://www.rhea-db.org/webservice|Rhea Web Services
		Added:
			REST|https://www.rhea-db.org/webservice|Rhea Web Services
		Removed:
			REST|http://www.rhea-db.org/rest/1.0/ws/reaction?q=caffeine|Rhea webservice

	'tools' has been modified:
		Before:
			ChemAxon||https://www.chemaxon.com/
			Metabolic Tinker||http://osslab.lifesci.warwick.ac.uk/tinker.aspx
			RxnSim|1.0.1|https://cran.r-project.org/web/packages/RxnSim/index.html
		After:
			ChemAxon||https://www.chemaxon.com/
			Metabolic Tinker||http://osslab.lifesci.warwick.ac.uk/tinker.aspx
			RxnSim|1.0.1|https://cran.r-project.org/web/packages/RxnSim/index.html
			SPARQL Endpoint||http://sparql.rhea-db.org/
		Added:
			SPARQL Endpoint||http://sparql.rhea-db.org/
		Removed:

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

Chemistry

ELIXIR Core Data and Data Deposition Resources

Support

General

contact form	Feedback Form
online documentation	Documentation
online documentation	Statistics

Additional Information

Contact	Anne Morgat
Identifiers.org	MIR:00000082

Tools

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

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Creative Commons Attribution 4.0 International (CC BY 4.0)

Data Release

Download Data

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

Data Curation

manual curation	No link recorded
Data Submission	https://www.rhea-db.org/submit

Data Access

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

REST Web Services

Rhea Web Services

https://www.rhea-db.org/webservice

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

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

Wellcome Open Research Data Guidelines

Credit

Record Maintainer

This record is maintained by amorgat

Funds

Swiss Federal Government (SERI) (Government body)
SystemsX.ch (Government body)
European Commission under FP7 Grant Agreement (Government body)

Maintains

Swiss Institute of Bioinformatics (SIB), Switzerland (Research institute)
European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK (Research institute)

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