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Protocols

Rhea specifications

Information


Unique identifier OMICS_06093
Name Rhea
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes

Documentation


Maintainer


  • person_outline Alan Bridge

Publications for Rhea

Rhea citations

 (5)
library_books

A review of computational tools for design and reconstruction of metabolic pathways

2017
PMCID: 5851934
PMID: 29552648
DOI: 10.1016/j.synbio.2017.11.002

[…] to constitute the pathway of interest. Currently, a number of databases have been constructed for known biochemical reactions and pathways (i.e., BIGG , KEGG , MetaCyc , BRENDA , ModelSEED , MetRxn , Rhea , UM-BBD , MOS , and Beilste Crossfile ), as well as hypothetical metabolites and reactions (such as ATLAS of Biochemistry , and MINE ) (see A). The current version of BIGG database consists of 8 […]

library_books

Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis

2016
Biophys Physicobiol
PMCID: 5042172
PMID: 27924274
DOI: 10.2142/biophysico.13.0_195

[…] trates and products may be listed exhaustively in the Enzyme List. Third, spontaneous reactions are not present in the Enzyme List.Many reaction databases (such as BRENDA [], KEGG [], MetaCyc [], and Rhea []) use the Enzyme List to reconstruct metabolic pathways and supplement with additional reactions to fill in the gaps. These reconstructed pathways can be represented as combined pathways that o […]

library_books

Reaction Decoder Tool (RDT): extracting features from chemical reactions

2016
Bioinformatics
PMCID: 4920114
PMID: 27153692
DOI: 10.1093/bioinformatics/btw096

[…] Large-scale chemical reaction databases such as KEGG (), BRENDA (), Rhea () and MetaCyc () link reactions to enzymes and provide data-mining opportunities for novel pathways (; ), and the discovery of drugs, natural products and green chemistry. One of the primary bot […]

library_books

The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases

2015
Nucleic Acids Res
PMCID: 4702916
PMID: 26615188
DOI: 10.1093/nar/gkv1310

[…] reference for the hierarchical enzymatic classification of the IUBMB/IUPAC joint nomenclature committee that is maintained by SIB. Explicit representations of enzymatic reactions are also provided by Rhea (www.ebi.ac.uk/rhea), a comprehensive and non-redundant resource of expert-curated biochemical reactions () described using species from the ChEBI (Chemical Entities of Biological Interest) ontol […]

call_split

The EBI enzyme portal

2012
Nucleic Acids Res
PMCID: 3531056
PMID: 23175605
DOI: 10.1093/nar/gks1112
call_split See protocol

[…] We used Java technologies—Spring Web MVC, JAXB, JAX-WS—and several Web Service APIs either SOAP—EB-Eye, ChEBI, CiteXplore—or REST—UniProt, Reactome, Rhea, ChEMBL, BioMart, DAS—to build the web application. XML schemas describe the underlying model.For quick cross-referencing and building filters for search results, an Oracle database was populated […]

Citations

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Rhea institution(s)
Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, Geneva, Switzerland; Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK; Department of Biochemistry, University of Geneva, Geneva, Switzerland; Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
Rhea funding source(s)
Supported by Swiss Federal Government through the State Secretariat for Education, Research and Innovation (SERI); SwissLipids project of the SystemsX.ch, the Swiss Initiative in Systems Biology (in part); EMBL and ELIXIR Implementation study on ‘A microbial metabolism resource for Systems Biology’ (in part).

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