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Suggestions for standardized identifiers for fatty acyl compounds in genome scale metabolic models and their application to the wormjam caenorhabditis elegans model.
Metabolites 10:130 (2020)
Genome scale metabolic models (GSMs) are a representation of the current knowledge on the metabolism of a given organism or superorganism. They group metabolites, genes, enzymes and reactions together to form a mathematical model and representation that can be used to analyze metabolic networks in silico or used for analysis of omics data. Beside correct mass and charge balance, correct structural annotation of metabolites represents an important factor for analysis of these metabolic networks. However, several metabolites in different GSMs have no or only partial structural information associated with them. Here, a new systematic nomenclature for acyl-based metabolites such as fatty acids, acyl-carnitines, acyl-coenzymes A or acyl-carrier proteins is presented. This nomenclature enables one to encode structural details in the metabolite identifiers and improves human readability of reactions. As proof of principle, it was applied to the fatty acid biosynthesis and degradation in the Caenorhabditis elegans consensus model WormJam.
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
Genome Scale Metabolic Networks ; Caenorhabditis Elegans ; Standardization; Reconstruction; Database; Network
ISSN (print) / ISBN
2218-1989
e-ISSN
2218-1989
Journal
Metabolites
Quellenangaben
Volume: 10,
Issue: 4,
Article Number: 130
Publisher
MDPI
Publishing Place
St Alban-anlage 66, Ch-4052 Basel, Switzerland
Non-patent literature
Publications
Reviewing status
Peer reviewed
Institute(s)
Research Unit Analytical BioGeoChemistry (BGC)