%0 Journal Article %1 May2013Metingear %A May, John W. %A James, A. Gordon %A Steinbeck, Christoph %D 2013 %J Bioinformatics %K genome-scale metabolic-networks reconstruction tool %N 17 %P 2213--2215 %R 10.1093/bioinformatics/btt342 %T Metingear: a development environment for annotating genome-scale metabolic models %U http://dx.doi.org/10.1093/bioinformatics/btt342 %V 29 %X Summary: 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 http://johnmay.github.com/metingear. The application is implemented in Java with bundles available for MS Windows and Macintosh OS X.Contact: johnmay@ebi.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.

@article{May2013Metingear, abstract = {Summary: 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 http://johnmay.github.com/metingear. The application is implemented in Java with bundles available for {MS} Windows and Macintosh {OS} {X.Contact}: {johnmay@ebi.ac.ukSupplementary} information: Supplementary data are available at Bioinformatics online.}, added-at = {2018-12-02T16:09:07.000+0100}, author = {May, John W. and James, A. Gordon and Steinbeck, Christoph}, biburl = {https://www.bibsonomy.org/bibtex/2ea8088d60876a90d9d9a92465703a451/karthikraman}, citeulike-article-id = {12438114}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btt342}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/29/17/2213}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/23766418}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=23766418}, day = 1, doi = {10.1093/bioinformatics/btt342}, interhash = {eef9123b6ffec21cc7c0efcdd9a5e09c}, intrahash = {ea8088d60876a90d9d9a92465703a451}, issn = {1367-4811}, journal = {Bioinformatics}, keywords = {genome-scale metabolic-networks reconstruction tool}, month = sep, number = 17, pages = {2213--2215}, pmid = {23766418}, posted-at = {2013-06-19 06:42:37}, priority = {2}, timestamp = {2018-12-02T16:09:07.000+0100}, title = {Metingear: a development environment for annotating genome-scale metabolic models}, url = {http://dx.doi.org/10.1093/bioinformatics/btt342}, volume = 29, year = 2013 }