Rhea-a manually curated resource of biochemical reactions

被引：72

作者：

Alcantara, Rafael ^{[1
]}

Axelsen, Kristian B. ^{[2
]}

Morgat, Anne ^{[2
,3
]}

Belda, Eugeni ^{[4
]}

Coudert, Elisabeth ^{[2
]}

Bridge, Alan ^{[2
]}

Cao, Hong ^{[1
]}

de Matos, Paula ^{[1
]}

Ennis, Marcus ^{[1
]}

Turner, Steve ^{[1
]}

Owen, Gareth ^{[1
]}

Bougueleret, Lydie ^{[2
]}

Xenarios, Ioannis ^{[2
,5
]}

Steinbeck, Christoph ^{[1
]}

机构：

[1] European Bioinformat Inst, Chemoinformat & Metab Team, Cambridge CB10 1SD, England

[2] SIB Swiss Inst Bioinformat, Swiss Prot Grp, CMU, CH-1211 Geneva 4, Switzerland

[3] INRIA Grenoble Rhone Alpes, Equipe BAMBOO, F-38330 Montbonnot St Martin, France

[4] CEA, Genoscope LABGeM, F-91057 Evry, France

[5] Swiss Inst Bioinformat, Vital IT, CH-1015 Lausanne, Switzerland

来源：

NUCLEIC ACIDS RESEARCH | 2012年 / 40卷 / D1期

关键词：

RECONSTRUCTION; NETWORKS; EXPLORATION; ANNOTATION; MECHANISM; PATHWAYS; DATABASE; ENZYMES;

D O I：

10.1093/nar/gkr1126

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Rhea (http://www.ebi.ac.uk/rhea) is a comprehensive resource of expert-curated biochemical reactions. Rhea provides a non-redundant set of chemical transformations for use in a broad spectrum of applications, including metabolic network reconstruction and pathway inference. Rhea includes enzyme-catalyzed reactions (covering the IUBMB Enzyme Nomenclature list), transport reactions and spontaneously occurring reactions. Rhea reactions are described using chemical species from the Chemical Entities of Biological Interest ontology (ChEBI) and are stoichiometrically balanced for mass and charge. They are extensively manually curated with links to source literature and other public resources on metabolism including enzyme and pathway databases. This cross-referencing facilitates the mapping and reconciliation of common reactions and compounds between distinct resources, which is a common first step in the reconstruction of genome scale metabolic networks and models.

引用

页码：D754 / D760

页数：7

共 26 条

[21] Challenges to be faced in the reconstruction of metabolic networks from public databases
Poolman, M. G.
Bonde, B. K.
Gevorgyan, A.
Patel, H. H.
Fell, D. A.
[J]. IEE PROCEEDINGS SYSTEMS BIOLOGY, 2006, 153 (05): : 379 - 384
[22] Integration of metabolic databases for the reconstruction of genome-scale metabolic networks
Radrich, Karin
Tsuruoka, Yoshimasa
Dobson, Paul
Gevorgyan, Albert
Swainston, Neil
Baart, Gino
Schwartz, Jean-Marc
[J]. BMC SYSTEMS BIOLOGY, 2010, 4
[23] Enabling the exploration of biochemical pathways
Reitz, M
Sacher, O
Tarkhov, A
Trümbach, D
Gasteiger, J
[J]. ORGANIC & BIOMOLECULAR CHEMISTRY, 2004, 2 (22) : 3226 - 3237
[24] Rijnbeek M.L., 2010, J CHEMINFORMATICS, V2, P28
[25] Rojas Isabel, 2007, In Silico Biology, V7, pS37
[26] BRENDA, the enzyme information system in 2011
Scheer, Maurice
Grote, Andreas
Chang, Antje
Schomburg, Ida
Munaretto, Cornelia
Rother, Michael
Soehngen, Carola
Stelzer, Michael
Thiele, Juliane
Schomburg, Dietmar
[J]. NUCLEIC ACIDS RESEARCH, 2011, 39 : D670 - D676

← 1 2 3 →