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. 2013 Sep 1;29(17):2213-5.
doi: 10.1093/bioinformatics/btt342. Epub 2013 Jun 13.

Metingear: A Development Environment for Annotating Genome-Scale Metabolic Models

Free PMC article

Metingear: A Development Environment for Annotating Genome-Scale Metabolic Models

John W May et al. Bioinformatics. .
Free PMC article


Genome-scale metabolic models often lack annotations that would allow them to be used for further analysis. Previous efforts have focused on associating metabolites in the model with a cross reference, but this can be problematic if the reference is not freely available, multiple resources are used or the metabolite is added from a literature review. Associating each metabolite with chemical structure provides unambiguous identification of the components and a more detailed view of the metabolism. We have developed an open-source desktop application that simplifies the process of adding database cross references and chemical structures to genome-scale metabolic models. Annotated models can be exported to the Systems Biology Markup Language open interchange format.

Availability: Source code, binaries, documentation and tutorials are freely available at The application is implemented in Java with bundles available for MS Windows and Macintosh OS X.


Fig. 1.
Fig. 1.
Overview of the annotation procedures to attach a chemical structure. Each method indicates whether the process is entirely automated, requires manual user input or combines an automated process with minimal user input

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