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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
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Updates in Rhea--a manually curated resource of biochemical reactions.
Anne Morgat1, Kristian B Axelsen2, Thierry Lombardot2
1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, CH-1206, Switzerland Genoscope-LABGeM, CEA, Evry, F-91057, France anne.morgat@isb-sib.ch.
Nucleic Acids Research
|October 22, 2014
Summary
Rhea, a biochemical reaction database, has expanded to include complex macromolecules, enhancing its utility for metabolic modeling and functional enzyme annotation. This growth supports better analysis and reconciliation of genome-scale metabolic networks.
Area of Science:
- Biochemistry
- Bioinformatics
- Systems Biology
Background:
- Rhea is an expert-curated database of biochemical reactions using the Chemical Entities of Biological Interest (ChEBI) ontology.
- It supports functional enzyme annotation and genome-scale metabolic network description.
Purpose of the Study:
- To report developments in the Rhea database since 2012.
- To highlight the inclusion of reactions involving complex macromolecules.
Main Methods:
- Expert curation of biochemical reactions.
- Mapping to other enzyme and pathway databases (Reactome, BioCyc, KEGG, UniPathway).
- Inclusion of reactions with macromolecules beyond ChEBI scope.
Main Results:
- Significant growth in the number of Rhea reactions.
- Expansion to include reactions involving proteins, nucleic acids, and polymers.
- Enhanced stoichiometric balancing for enzyme-catalyzed, transport, and spontaneous reactions.
Conclusions:
- The expanded Rhea database offers increased utility for describing, analyzing, and reconciling genome-scale metabolic models.
- The inclusion of macromolecule reactions broadens its applicability in biological research.
- Rhea continues to be a vital resource for biochemical data integration and analysis.
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