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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)

Bottom Line: Here we describe developments in Rhea since our last report in the 2012 database issue of Nucleic Acids Research.These include significant growth in the number of Rhea reactions and the inclusion of reactions involving complex macromolecules such as proteins, nucleic acids and other polymers that lie outside the scope of ChEBI.Together these developments will significantly increase the utility of Rhea as a tool for the description, analysis and reconciliation of genome-scale metabolic models.

View Article: PubMed Central - PubMed

Affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, CH-1206, Switzerland Genoscope-LABGeM, CEA, Evry, F-91057, France anne.morgat@isb-sib.ch.

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Interactions between Rhea and other resources. Rhea provides cross-references to chemical entities of ChEBI (2), to biochemical reactions of EcoCyc (19), MetaCyc (20), KEGG (18), MACiE (16), Reactome (17) and UniPathway (21), to EC numbers of IntEnz (10) and to protein sequences of UniProtKB (15). The Gene Ontology (GO) is closely aligned with ChEBI , and GO molecular functions describing enzymatic reactions cross-reference Rhea (29). Rhea is one of the reaction repositories employed by MicroScope (9), an integrated resource for the curation and comparative analysis of genomic and metabolic data of microbes. Rhea also provides metabolic reactions for a number of other resources including the EBI Enzyme Portal (5), the reference layer of the MetaboLights resource (6), the metabolic model analysis and reconciliation platform of MetaNetX.org (7,8), EC-BLAST (11) and Metabolic tinker (12).
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Figure 1: Interactions between Rhea and other resources. Rhea provides cross-references to chemical entities of ChEBI (2), to biochemical reactions of EcoCyc (19), MetaCyc (20), KEGG (18), MACiE (16), Reactome (17) and UniPathway (21), to EC numbers of IntEnz (10) and to protein sequences of UniProtKB (15). The Gene Ontology (GO) is closely aligned with ChEBI , and GO molecular functions describing enzymatic reactions cross-reference Rhea (29). Rhea is one of the reaction repositories employed by MicroScope (9), an integrated resource for the curation and comparative analysis of genomic and metabolic data of microbes. Rhea also provides metabolic reactions for a number of other resources including the EBI Enzyme Portal (5), the reference layer of the MetaboLights resource (6), the metabolic model analysis and reconciliation platform of MetaNetX.org (7,8), EC-BLAST (11) and Metabolic tinker (12).

Mentions: Rhea is a manually curated resource of biochemical reactions for the functional annotation of enzymes and the description of genome-scale metabolic networks (1). Rhea provides stoichiometrically balanced descriptions for enzyme-catalyzed reactions, transport reactions and spontaneously occurring reactions using chemical species from the Chemical Entities of Biological Interest (ChEBI) ontology (2), specifying reaction constituents, their stoichiometric coefficients and relative locations. This information is manually curated from peer-reviewed literature by experts. Each Rhea reaction is assigned a unique identifier, with uniqueness ensured by the calculation of a fingerprint for each reaction which considers the constituent compounds, their stoichiometry and localization. Reaction constituents are represented by the major micro-species at pH 7.3 (verified using the Marvin pKa calculator from ChemAxon (version 6.2.0, http://www.chemaxon.com)). All reactions are stoichiometrically balanced for both mass and charge, which facilitates the use of Rhea for the construction, analysis, comparison and reconciliation of genome-scale metabolic models (3,4). More details on the representation of reactions can be found in our preceding paper (1). Rhea provides metabolic reactions for a number of other biological data and knowledge resources including the EBI Enzyme Portal (5), the reference layer of the MetaboLights resource (6), the metabolic model analysis and reconciliation platform of MetaNetX.org (7,8), the microbial genomic annotation platform MicroScope (9) and IntEnz, a reference for the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzymes (10). Rhea reactions are also used by tools such as EC-BLAST, a tool to automatically search and compare biochemical reactions (11) as well as Metabolic tinker (12), an online tool for guiding the design of synthetic metabolic pathways. Interactions between Rhea and other resources are described in Figure 1.


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)

Interactions between Rhea and other resources. Rhea provides cross-references to chemical entities of ChEBI (2), to biochemical reactions of EcoCyc (19), MetaCyc (20), KEGG (18), MACiE (16), Reactome (17) and UniPathway (21), to EC numbers of IntEnz (10) and to protein sequences of UniProtKB (15). The Gene Ontology (GO) is closely aligned with ChEBI , and GO molecular functions describing enzymatic reactions cross-reference Rhea (29). Rhea is one of the reaction repositories employed by MicroScope (9), an integrated resource for the curation and comparative analysis of genomic and metabolic data of microbes. Rhea also provides metabolic reactions for a number of other resources including the EBI Enzyme Portal (5), the reference layer of the MetaboLights resource (6), the metabolic model analysis and reconciliation platform of MetaNetX.org (7,8), EC-BLAST (11) and Metabolic tinker (12).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384025&req=5

Figure 1: Interactions between Rhea and other resources. Rhea provides cross-references to chemical entities of ChEBI (2), to biochemical reactions of EcoCyc (19), MetaCyc (20), KEGG (18), MACiE (16), Reactome (17) and UniPathway (21), to EC numbers of IntEnz (10) and to protein sequences of UniProtKB (15). The Gene Ontology (GO) is closely aligned with ChEBI , and GO molecular functions describing enzymatic reactions cross-reference Rhea (29). Rhea is one of the reaction repositories employed by MicroScope (9), an integrated resource for the curation and comparative analysis of genomic and metabolic data of microbes. Rhea also provides metabolic reactions for a number of other resources including the EBI Enzyme Portal (5), the reference layer of the MetaboLights resource (6), the metabolic model analysis and reconciliation platform of MetaNetX.org (7,8), EC-BLAST (11) and Metabolic tinker (12).
Mentions: Rhea is a manually curated resource of biochemical reactions for the functional annotation of enzymes and the description of genome-scale metabolic networks (1). Rhea provides stoichiometrically balanced descriptions for enzyme-catalyzed reactions, transport reactions and spontaneously occurring reactions using chemical species from the Chemical Entities of Biological Interest (ChEBI) ontology (2), specifying reaction constituents, their stoichiometric coefficients and relative locations. This information is manually curated from peer-reviewed literature by experts. Each Rhea reaction is assigned a unique identifier, with uniqueness ensured by the calculation of a fingerprint for each reaction which considers the constituent compounds, their stoichiometry and localization. Reaction constituents are represented by the major micro-species at pH 7.3 (verified using the Marvin pKa calculator from ChemAxon (version 6.2.0, http://www.chemaxon.com)). All reactions are stoichiometrically balanced for both mass and charge, which facilitates the use of Rhea for the construction, analysis, comparison and reconciliation of genome-scale metabolic models (3,4). More details on the representation of reactions can be found in our preceding paper (1). Rhea provides metabolic reactions for a number of other biological data and knowledge resources including the EBI Enzyme Portal (5), the reference layer of the MetaboLights resource (6), the metabolic model analysis and reconciliation platform of MetaNetX.org (7,8), the microbial genomic annotation platform MicroScope (9) and IntEnz, a reference for the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzymes (10). Rhea reactions are also used by tools such as EC-BLAST, a tool to automatically search and compare biochemical reactions (11) as well as Metabolic tinker (12), an online tool for guiding the design of synthetic metabolic pathways. Interactions between Rhea and other resources are described in Figure 1.

Bottom Line: Here we describe developments in Rhea since our last report in the 2012 database issue of Nucleic Acids Research.These include significant growth in the number of Rhea reactions and the inclusion of reactions involving complex macromolecules such as proteins, nucleic acids and other polymers that lie outside the scope of ChEBI.Together these developments will significantly increase the utility of Rhea as a tool for the description, analysis and reconciliation of genome-scale metabolic models.

View Article: PubMed Central - PubMed

Affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, CH-1206, Switzerland Genoscope-LABGeM, CEA, Evry, F-91057, France anne.morgat@isb-sib.ch.

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