{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,22]],"date-time":"2025-12-22T05:48:22Z","timestamp":1766382502689,"version":"3.37.3"},"reference-count":12,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,4,21]],"date-time":"2021-04-21T00:00:00Z","timestamp":1618963200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2021,4,21]],"date-time":"2021-04-21T00:00:00Z","timestamp":1618963200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["GM080746"],"award-info":[{"award-number":["GM080746"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>The Metabolic Network Explorer is a new addition to the BioCyc.org website and the Pathway Tools software suite that supports the interactive exploration of metabolic networks. Any metabolic network visualization tool must by necessity show only a subset of all possible metabolite connections, or the results will be visually overwhelming. Existing tools, even those that purport to show an organism\u2019s full metabolic network, limit the set of displayed connections based on predefined pathways or other preselected criteria. We sought instead to provide a tool that would give the user dynamic control over which connections to follow.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The Metabolic Network Explorer is an easy-to-use, web-based software tool that allows the user to specify a starting metabolite of interest and interactively explore its immediate metabolic neighborhood in either or both directions to any desired depth, letting the user select from the full set of connected reactions. Although, as for other tools, only a small portion of the metabolic network is visible at a time, that portion is selected by the user, based on the full reaction complement, and it is easy to switch among alternate paths of interest. The display is intuitive, customizable, and provides copious links to more detailed information pages.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>The Metabolic Network Explorer fills a gap in the set of metabolic network visualization tools and complements other modes of exploration. Its primary strengths are its ease of use, diagrams that are intuitive to biologists, and its integration with the broader corpus of data provided by a BioCyc Pathway\/Genome Database.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-021-04132-5","type":"journal-article","created":{"date-parts":[[2021,4,21]],"date-time":"2021-04-21T12:22:32Z","timestamp":1619007752000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["The BioCyc Metabolic Network Explorer"],"prefix":"10.1186","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5763-8935","authenticated-orcid":false,"given":"Suzanne","family":"Paley","sequence":"first","affiliation":[]},{"given":"Peter D.","family":"Karp","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2021,4,21]]},"reference":[{"issue":"D1","key":"4132_CR1","doi-asserted-by":"publisher","first-page":"D633","DOI":"10.1093\/nar\/gkx935","volume":"46","author":"R Caspi","year":"2018","unstructured":"Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD. The MetaCyc database of metabolic pathways and enzymes. Nucl Acids Res. 2018;46(D1):D633-39.","journal-title":"Nucl Acids Res"},{"issue":"2","key":"4132_CR2","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1093\/bioinformatics\/btx588","volume":"34","author":"M Chazalviel","year":"2018","unstructured":"Chazalviel M, Frainay C, Poupin N, Vinson F, Merlet B, Gloaguen Y, Cottret L, Jourdan F. MetExploreViz: web component for interactive metabolic network visualization. Bioinformatics. 2018;34(2):312\u20133.","journal-title":"Bioinformatics"},{"issue":"D1","key":"4132_CR3","first-page":"D498","volume":"48","author":"B Jassal","year":"2020","unstructured":"Jassal B, Matthews L, Viteri G, Gong C, Lorente P, Fabregat A, Sidiropoulos K, Cook J, Gillespie M, Haw R, Loney F, May B, Milacic M, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Weiser J, Wu G, Stein L, Hermjakob H, D\u2019Eustachio P. The Reactome pathway knowledgebase. Nucl Acids Res. 2020;48(D1):D498\u2013503.","journal-title":"Nucl Acids Res"},{"issue":"Database issue","key":"4132_CR4","doi-asserted-by":"publisher","first-page":"D542","DOI":"10.1093\/nar\/gky1048","volume":"47","author":"L Jeske","year":"2019","unstructured":"Jeske L, Placzek S, Schomburg I, Chang A, Schomburg D. BRENDA in 2019: a European ELIXIR core data resource. Nucl Acids Res. 2019;47(Database issue):D542-49.","journal-title":"Nucl Acids Res"},{"issue":"Database issue","key":"4132_CR5","doi-asserted-by":"publisher","first-page":"D478","DOI":"10.1093\/nar\/gkt1067","volume":"42","author":"T Jewison","year":"2014","unstructured":"Jewison T, Su Y, Disfany FM, Liang Y, Knox C, Maciejewski A, Poelzer J, Huynh J, Zhou Y, Arndt D, Djoumbou Y, Liu Y, Deng L, Guo AC, Han B, Pon A, Wilson M, Rafatnia S, Liu P, Wishart DS. SMPDB 2.0: big improvements to the small molecule pathway database. Nucl Acids Res. 2014;42(Database issue):D478-84.","journal-title":"Nucl Acids Res"},{"issue":"Database issue","key":"4132_CR6","doi-asserted-by":"publisher","first-page":"D199","DOI":"10.1093\/nar\/gkt1076","volume":"42","author":"M Kanehisa","year":"2014","unstructured":"Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M. Data, information, knowledge and principle: back to metabolism in KEGG. Nucl Acids Res. 2014;42(Database issue):D199\u2013205.","journal-title":"Nucl Acids Res"},{"key":"4132_CR7","doi-asserted-by":"publisher","first-page":"1085","DOI":"10.1093\/bib\/bbx085","volume":"20","author":"PD Karp","year":"2017","unstructured":"Karp PD, Billington R, Caspi R, Fulcher CA, Latendresse M, Kothari A, Keseler IM, Krummenacker M, Midford PE, Ong Q, Ong WK, Paley SM, Subhraveti P. The BioCyc collection of microbial genomes and metabolic pathways. Brief Bioinform. 2017;20:1085\u201393. https:\/\/doi.org\/10.1093\/bib\/bbx085.","journal-title":"Brief Bioinform"},{"key":"4132_CR8","doi-asserted-by":"crossref","unstructured":"Karp PD, Midford PE, Paley SM, Krummenacker M, Billington R, Kothari A, Ong WK, Subhraveti P, Keseler IM, Caspi R. Pathway tools version 24.0: integrated software for pathway\/genome informatics and systems biology [v4]. 2020. p. 1\u201398. arXiv arXiv:1510.03964v4","DOI":"10.1093\/bib\/bbz104"},{"key":"4132_CR9","unstructured":"KEGG Metabolic Chart. https:\/\/www.kegg.jp\/kegg-bin\/show_pathway?map01100."},{"issue":"2","key":"4132_CR10","doi-asserted-by":"publisher","first-page":"64","DOI":"10.3390\/metabo11020064","volume":"11","author":"S Paley","year":"2021","unstructured":"Paley S, Billington R, Herson J, Krummenacker M, Karp PD. Pathway tools visualization of organism-scale metabolic networks. 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