Abstract
BackgroundIncreasingly, metabolite and reaction information is organized in the form of genome-scale metabolic reconstructions that describe the reaction stoichiometry, directionality, and gene to protein to reaction associations. A key bottleneck in the pace of reconstruction of new, high-quality metabolic models is the inability to directly make use of metabolite/reaction information from biological databases or other models due to incompatibilities in content representation (i.e., metabolites with multiple names across databases and models), stoichiometric errors such as elemental or charge imbalances, and incomplete atomistic detail (e.g., use of generic R-group or non-explicit specification of stereo-specificity).DescriptionMetRxn is a knowledgebase that includes standardized metabolite and reaction descriptions by integrating information from BRENDA, KEGG, MetaCyc, Reactome.org and 44 metabolic models into a single unified data set. All metabolite entries have matched synonyms, resolved protonation states, and are linked to unique structures. All reaction entries are elementally and charge balanced. This is accomplished through the use of a workflow of lexicographic, phonetic, and structural comparison algorithms. MetRxn allows for the download of standardized versions of existing genome-scale metabolic models and the use of metabolic information for the rapid reconstruction of new ones.ConclusionsThe standardization in description allows for the direct comparison of the metabolite and reaction content between metabolic models and databases and the exhaustive prospecting of pathways for biotechnological production. This ever-growing dataset currently consists of over 76,000 metabolites participating in more than 72,000 reactions (including unresolved entries). MetRxn is hosted on a web-based platform that uses relational database models (MySQL).
Highlights
Introduction to methodology and encoding rulesJournal of Chemical Information and Computer Sciences 1988, 28(1):31-36.39
Metabolite and reaction information is organized in the form of community [2], organism, or even tissue-specific genome-scale metabolic reconstructions
These reconstructions account for reaction stoichiometry and directionality, gene to protein to reaction associations, organelle reaction localization, transporter information, transcriptional regulation
Summary
MetRxn enables the standardization, correction and utilization of rapidly growing metabolic information for over 76,000 metabolites participating in 72,000 reactions (including unresolved entries). The standardization of published genome-scale models enables the rapidly growing community of researchers who make use of metabolic information to understand metabolism at an organism-level and re-deploy it for various biotechnological objectives. During the construction of the initial release of MetRxn, we managed to associate structures for over 8,800 metabolites and re-balanced more than 2,400 reaction instances across 44 metabolic models. This enables the genuine comparison of metabolic content between metabolic models.
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