{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T14:12:32Z","timestamp":1740147152960,"version":"3.37.3"},"reference-count":25,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,11,29]],"date-time":"2016-11-29T00:00:00Z","timestamp":1480377600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2016,11,29]],"date-time":"2016-11-29T00:00:00Z","timestamp":1480377600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["EEC-0813570"],"award-info":[{"award-number":["EEC-0813570"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["ABI-1062546"],"award-info":[{"award-number":["ABI-1062546"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["IOS-1026003"],"award-info":[{"award-number":["IOS-1026003"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-SC0008769"],"award-info":[{"award-number":["DE-SC0008769"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U01 GM110699"],"award-info":[{"award-number":["U01 GM110699"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000199","name":"U.S. Department of Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2016,12]]},"DOI":"10.1186\/s12918-016-0369-x","type":"journal-article","created":{"date-parts":[[2016,11,29]],"date-time":"2016-11-29T13:42:16Z","timestamp":1480426936000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize"],"prefix":"10.1186","volume":"10","author":[{"given":"Jesse R.","family":"Walsh","sequence":"first","affiliation":[]},{"given":"Mary L.","family":"Schaeffer","sequence":"additional","affiliation":[]},{"given":"Peifen","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Seung Y.","family":"Rhee","sequence":"additional","affiliation":[]},{"given":"Julie A.","family":"Dickerson","sequence":"additional","affiliation":[]},{"given":"Taner Z.","family":"Sen","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,11,29]]},"reference":[{"issue":"D1","key":"369_CR1","doi-asserted-by":"publisher","first-page":"1049","DOI":"10.1093\/nar\/gku1179","volume":"43","author":"TGO Consortium","year":"2015","unstructured":"Consortium TGO. Gene Ontology Consortium: going forward. Nucleic Acids Res. 2015; 43(D1):1049\u201356. doi:\n                    10.1093\/nar\/gku1179\n                    \n                  .","journal-title":"Nucleic Acids Res"},{"key":"369_CR2","volume-title":"Enzyme nomenclature 1992. Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes","author":"EC Webb","year":"1992","unstructured":"Webb EC. Enzyme nomenclature 1992. Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes, 6th ed. San Diego: Academic Press; 1992."},{"issue":"2","key":"369_CR3","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1093\/bib\/2.2.126","volume":"2","author":"U Wittig","year":"2001","unstructured":"Wittig U, Beuckelaer AD. Analysis and comparison of metabolic pathway databases. Brief Bioinform. 2001; 2(2):126\u201342. doi:\n                    10.1093\/bib\/2.2.126\n                    \n                  .","journal-title":"Brief Bioinform"},{"key":"369_CR4","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1186\/1471-2105-7-170","volume":"7","author":"TJ Lee","year":"2006","unstructured":"Lee TJ, Pouliot Y, Wagner V, Gupta P, Stringer-Calvert DW, Tenenbaum JD, Karp PD. BioWarehouse: a bioinformatics database warehouse toolkit. BMC Bioinforma. 2006; 7:170. doi:\n                    10.1186\/1471-2105-7-170\n                    \n                  .","journal-title":"BMC Bioinforma"},{"issue":"1","key":"369_CR5","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/1471-2105-13-6","volume":"13","author":"A Kumar","year":"2012","unstructured":"Kumar A, Suthers PF, Maranas CD. MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. BMC Bioinforma. 2012; 13(1):6. doi:\n                    10.1186\/1471-2105-13-6\n                    \n                  .","journal-title":"BMC Bioinforma"},{"issue":"1","key":"369_CR6","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1186\/1471-2105-14-112","volume":"14","author":"T Altman","year":"2013","unstructured":"Altman T, Travers M, Kothari A, Caspi R, Karp PD. A systematic comparison of the MetaCyc and KEGG pathway databases. BMC Bioinforma. 2013; 14(1):112. doi:\n                    10.1186\/1471-2105-14-112\n                    \n                  .","journal-title":"BMC Bioinforma"},{"issue":"5956","key":"369_CR7","doi-asserted-by":"publisher","first-page":"1112","DOI":"10.1126\/science.1178534","volume":"326","author":"PS Schnable","year":"2009","unstructured":"Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Buren PV, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK. The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science. 2009; 326(5956):1112\u20135. doi:\n                    10.1126\/science.1178534\n                    \n                  .","journal-title":"Science"},{"issue":"suppl 1","key":"369_CR8","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1093\/bioinformatics\/18.suppl_1.S225","volume":"18","author":"PD Karp","year":"2002","unstructured":"Karp PD, Paley S, Romero P. The Pathway Tools software. Bioinformatics. 2002; 18(suppl 1):225\u201332. doi:\n                    10.1093\/bioinformatics\/18.suppl_1.S225\n                    \n                  .","journal-title":"Bioinformatics"},{"issue":"6183","key":"369_CR9","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1126\/science.1252076","volume":"344","author":"L Chae","year":"2014","unstructured":"Chae L, Kim T, Nilo-Poyanco R, Rhee SY. Genomic signatures of specialized metabolism in plants. Science (New York, N.Y.) 2014; 344(6183):510\u20133. doi:\n                    10.1126\/science.1252076\n                    \n                  .","journal-title":"Science (New York, N.Y.)"},{"issue":"4","key":"369_CR10","doi-asserted-by":"publisher","first-page":"1479","DOI":"10.1104\/pp.110.157396","volume":"153","author":"P Zhang","year":"2010","unstructured":"Zhang P, Dreher K, Karthikeyan A, Chi A, Pujar A, Caspi R, Karp P, Kirkup V, Latendresse M, Lee C, Mueller LA, Muller R, Rhee SY. Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants 1[W][OA]. Plant Physiol. 2010; 153(4):1479\u201391. doi:\n                    10.1104\/pp.110.157396\n                    \n                  .","journal-title":"Plant Physiol"},{"key":"369_CR11","doi-asserted-by":"crossref","unstructured":"Sen TZ, Andorf CM, Schaeffer ML, Harper LC, Sparks ME, Duvick J, Brendel VP, Cannon E, Campbell DA, Lawrence CJ. MaizeGDB becomes \u2019sequence-centric\u2019. Database: J Biol Databases Curation. 2009; 2009. doi:\n                    10.1093\/database\/bap020\n                    \n                  .","DOI":"10.1093\/database\/bap020"},{"issue":"D1","key":"369_CR12","doi-asserted-by":"publisher","first-page":"1195","DOI":"10.1093\/nar\/gkv1007","volume":"44","author":"CM Andorf","year":"2016","unstructured":"Andorf CM, Cannon EK, Portwood JL, Gardiner JM, Harper LC, Schaeffer ML, Braun BL, Campbell DA, Vinnakota AG, Sribalusu VV, Huerta M, Cho KT, Wimalanathan K, Richter JD, Mauch ED, Rao BS, Birkett SM, Sen TZ, Lawrence-Dill CJ. MaizeGDB update: new tools, data and interface for the maize model organism database. Nucleic Acids Res. 2016; 44(D1):1195\u2013201. doi:\n                    10.1093\/nar\/gkv1007\n                    \n                  .","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"369_CR13","doi-asserted-by":"publisher","first-page":"0","DOI":"10.3835\/plantgenome2012.09.0025","volume":"6","author":"MK Monaco","year":"2013","unstructured":"Monaco MK, Sen TZ, Dharmawardhana PD, Ren L, Schaeffer M, Naithani S, Amarasinghe V, Thomason J, Harper L, Gardiner J, Cannon EKS, Lawrence CJ, Ware D, Jaiswal P. Maize Metabolic Network Construction and Transcriptome Analysis. Plant Genome. 2013; 6(1):0. doi:\n                    10.3835\/plantgenome2012.09.0025\n                    \n                  .","journal-title":"Plant Genome"},{"key":"369_CR14","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1186\/1471-2105-6-31","volume":"6","author":"GSC Slater","year":"2005","unstructured":"Slater GSC, Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinforma. 2005; 6:31. doi:\n                    10.1186\/1471-2105-6-31\n                    \n                  .","journal-title":"BMC Bioinforma"},{"issue":"D1","key":"369_CR15","doi-asserted-by":"publisher","first-page":"662","DOI":"10.1093\/nar\/gku1010","volume":"43","author":"F Cunningham","year":"2015","unstructured":"Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Gir\u00f3n CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, K\u00e4h\u00e4ri AK, Keenan S, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Overduin B, Parker A, Patricio M, Perry E, Pignatelli M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Aken BL, Birney E, Harrow J, Kinsella R, Muffato M, Ruffier M, Searle SMJ, Spudich G, Trevanion SJ, Yates A, Zerbino DR, Flicek P. Ensembl 2015. Nucleic Acids Res. 2015; 43(D1):662\u20139. doi:\n                    10.1093\/nar\/gku1010\n                    \n                  .","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"369_CR16","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1093\/nar\/gku989","volume":"43","author":"TU Consortium","year":"2015","unstructured":"Consortium TU. UniProt: a hub for protein information. Nucleic Acids Res. 2015; 43(D1):204\u201312. doi:\n                    10.1093\/nar\/gku989\n                    \n                  .","journal-title":"Nucleic Acids Res"},{"key":"369_CR17","doi-asserted-by":"crossref","unstructured":"Chang A, Schomburg I, Placzek S, Jeske L, Ulbrich M, Xiao M, Sensen CW, Schomburg D. BRENDA in 2015: exciting developments in its 25th year of existence. Nucleic Acids Res. 2014:1068. doi:\n                    10.1093\/nar\/gku1068\n                    \n                  .","DOI":"10.1093\/nar\/gku1068"},{"issue":"18","key":"369_CR18","doi-asserted-by":"publisher","first-page":"2345","DOI":"10.1093\/bioinformatics\/btq423","volume":"26","author":"JL Van Hemert","year":"2010","unstructured":"Van Hemert JL, Dickerson JA. PathwayAccess: CellDesigner plugins for pathway databases. Bioinformatics. 2010; 26(18):2345\u20136. doi:\n                    10.1093\/bioinformatics\/btq423\n                    \n                  .","journal-title":"Bioinformatics"},{"issue":"3","key":"369_CR19","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990; 215(3):403\u201310. doi:\n                    10.1016\/S0022-2836(05)80360-2\n                    \n                  .","journal-title":"J Mol Biol"},{"issue":"2","key":"369_CR20","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1002\/prot.22167","volume":"74","author":"C Yu","year":"2009","unstructured":"Yu C, Zavaljevski N, Desai V, Reifman J. Genome-wide enzyme annotation with precision control: catalytic families (CatFam) databases. Proteins. 2009; 74(2):449\u201360. doi:\n                    10.1002\/prot.22167\n                    \n                  .","journal-title":"Proteins"},{"issue":"22","key":"369_CR21","doi-asserted-by":"publisher","first-page":"6633","DOI":"10.1093\/nar\/gkg847","volume":"31","author":"C Claudel-Renard","year":"2003","unstructured":"Claudel-Renard C, Chevalet C, Faraut T, Kahn D. Enzyme-specific profiles for genome annotation: PRIAM. Nucleic Acids Res. 2003; 31(22):6633\u20139. doi:\n                    10.1093\/nar\/gkg847\n                    \n                  .","journal-title":"Nucleic Acids Res"},{"key":"369_CR22","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1007\/978-1-4939-3167-5_2","volume":"1374","author":"E Boutet","year":"2016","unstructured":"Boutet E, Lieberherr D, Tognolli M, Schneider M, Bansal P, Bridge AJ, Poux S, Bougueleret L, Xenarios I. UniProtKB\/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View. Methods Mol Biol (Clifton, N.J.) 2016; 1374:23\u201354. doi:\n                    10.1007\/978-1-4939-3167-5_2\n                    \n                  .","journal-title":"Methods Mol Biol (Clifton, N.J.)"},{"issue":"D1","key":"369_CR23","doi-asserted-by":"publisher","first-page":"459","DOI":"10.1093\/nar\/gkt1103","volume":"42","author":"R Caspi","year":"2014","unstructured":"Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway\/Genome Databases. Nucleic Acids Res. 2014; 42(D1):459\u201371. doi:\n                    10.1093\/nar\/gkt1103\n                    \n                  .","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"369_CR24","doi-asserted-by":"publisher","first-page":"17855","DOI":"10.1371\/journal.pone.0017855","volume":"6","author":"JC Schnable","year":"2011","unstructured":"Schnable JC, Freeling M. Genes Identified by Visible Mutant Phenotypes Show Increased Bias toward One of Two Subgenomes of Maize. PLoS ONE. 2011; 6(3):17855. doi:\n                    10.1371\/journal.pone.0017855\n                    \n                  .","journal-title":"PLoS ONE"},{"issue":"1","key":"369_CR25","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1186\/s12918-014-0115-1","volume":"8","author":"JR Walsh","year":"2014","unstructured":"Walsh JR, Sen TZ, Dickerson JA. A computational platform to maintain and migrate manual functional annotations for BioCyc databases. BMC Syst Biol. 2014; 8(1):115. doi:\n                    10.1186\/s12918-014-0115-1\n                    \n                  .","journal-title":"BMC Syst Biol"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-016-0369-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12918-016-0369-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-016-0369-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,15]],"date-time":"2020-05-15T10:43:22Z","timestamp":1589539402000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/s12918-016-0369-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,11,29]]},"references-count":25,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2016,12]]}},"alternative-id":["369"],"URL":"https:\/\/doi.org\/10.1186\/s12918-016-0369-x","relation":{},"ISSN":["1752-0509"],"issn-type":[{"type":"electronic","value":"1752-0509"}],"subject":[],"published":{"date-parts":[[2016,11,29]]},"assertion":[{"value":"12 July 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 November 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 November 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"129"}}