Data, information, knowledge and principle: back to metabolism in KEGG
TL;DR: The reaction modules, which represent chemical units of reactions, have been used to analyze design principles of metabolic networks and also to improve the definition of K numbers and associated annotations for translational bioinformatics.
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Abstract: In the hierarchy of data, information and knowledge, computational methods play a major role in the initial processing of data to extract information, but they alone become less effective to compile knowledge from information. The Kyoto Encyclopedia of Genes and Genomes (KEGG) resource (http://www.kegg.jp/ or http://www.genome.jp/kegg/) has been developed as a reference knowledge base to assist this latter process. In particular, the KEGG pathway maps are widely used for biological interpretation of genome sequences and other high-throughput data. The link from genomes to pathways is made through the KEGG Orthology system, a collection of manually defined ortholog groups identified by K numbers. To better automate this interpretation process the KEGG modules defined by Boolean expressions of K numbers have been expanded and improved. Once genes in a genome are annotated with K numbers, the KEGG modules can be computationally evaluated revealing metabolic capacities and other phenotypic features. The reaction modules, which represent chemical units of reactions, have been used to analyze design principles of metabolic networks and also to improve the definition of K numbers and associated annotations. For translational bioinformatics, the KEGG MEDICUS resource has been developed by integrating drug labels (package inserts) used in society.
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References
KEGG for integration and interpretation of large-scale molecular data sets
TL;DR: KEGG Mapper, a collection of tools for KEGG PATHWAY, BRITE and MODULE mapping, enabling integration and interpretation of large-scale data sets and recent enhancements to the K EGG content, especially the incorporation of disease and drug information used in practice and in society, to support translational bioinformatics.
ExplorEnz: the primary source of the IUBMB enzyme list
TL;DR: ExplorEnz is the MySQL database that is used for the curation and dissemination of the IUBMB Enzyme Nomenclature and an associated form-based curatorial application has been developed to facilitate the curations of enzyme data.
Modular architecture of metabolic pathways revealed by conserved sequences of reactions.
TL;DR: A method to extract conserved sequences of reactions called reaction modules from the analysis of chemical compound structure transformation patterns in all known metabolic pathways stored in the KEGG PATHWAY database is developed.
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ORENZA: a web resource for studying ORphan ENZyme activities.
Olivier Lespinet,Bernard Labedan +1 more
TL;DR: ORENZA is a Web resource designed to progressively bridge the unwanted gap between function (enzyme activities) and sequence (dataset present in public databases) and should increase interactions between communities of biochemists and of genomicists.
Chemical and genomic evolution of enzyme-catalyzed reaction networks.
TL;DR: It is shown that a unit of enzyme genes in an operon‐like structure in the prokaryotic genome encodes enzymes that catalyze a series of consecutive reactions in a metabolic pathway correspond to chemical units reflecting chemical logic of organic reactions.
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