{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T06:20:08Z","timestamp":1791181208995,"version":"4.1.0"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1207,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Contact: \u00a0johnmay@ebi.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt342","type":"journal-article","created":{"date-parts":[[2013,6,14]],"date-time":"2013-06-14T00:38:58Z","timestamp":1371170338000},"page":"2213-2215","source":"Crossref","is-referenced-by-count":7,"title":["Metingear: a development environment for annotating genome-scale metabolic models"],"prefix":"10.1093","volume":"29","author":[{"given":"John W.","family":"May","sequence":"first","affiliation":[{"name":"1 Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and 2Unilever Discover, Colworth Science Park, Bedford, MK44 1LQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A. Gordon","family":"James","sequence":"additional","affiliation":[{"name":"1 Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and 2Unilever Discover, Colworth Science Park, Bedford, MK44 1LQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christoph","family":"Steinbeck","sequence":"additional","affiliation":[{"name":"1 Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and 2Unilever Discover, Colworth Science Park, Bedford, MK44 1LQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,6,13]]},"reference":[{"key":"2023012810455865800_btt342-B1","doi-asserted-by":"crossref","first-page":"2763","DOI":"10.1093\/bioinformatics\/btr456","article-title":"Metannogen: annotation of biological reaction networks","volume":"27","author":"Gille","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012810455865800_btt342-B2","doi-asserted-by":"crossref","first-page":"D456","DOI":"10.1093\/nar\/gks1146","article-title":"The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013","volume":"41","author":"Hastings","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023012810455865800_btt342-B3","doi-asserted-by":"crossref","first-page":"969","DOI":"10.1038\/nbt.1672","article-title":"High-throughput generation, optimization and analysis of genome-scale metabolic models","volume":"28","author":"Henry","year":"2010","journal-title":"Nat. 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