{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T00:30:18Z","timestamp":1779237018275,"version":"3.51.4"},"reference-count":33,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2015,7,11]],"date-time":"2015-07-11T00:00:00Z","timestamp":1436572800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["ID0EG3BG68"],"award-info":[{"award-number":["ID0EG3BG68"]}],"id":[{"id":"10.13039\/501100000268","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":[[2015,12]]},"DOI":"10.1186\/s12918-015-0174-y","type":"journal-article","created":{"date-parts":[[2015,7,9]],"date-time":"2015-07-09T21:21:47Z","timestamp":1436476907000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":85,"title":["SEEK: a systems biology data and model management platform"],"prefix":"10.1186","volume":"9","author":[{"given":"Katherine","family":"Wolstencroft","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stuart","family":"Owen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olga","family":"Krebs","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Quyen","family":"Nguyen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Natalie J","family":"Stanford","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Golebiewski","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Weidemann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meik","family":"Bittkowski","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lihua","family":"An","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Shockley","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jacky L.","family":"Snoep","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wolfgang","family":"Mueller","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carole","family":"Goble","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2015,7,11]]},"reference":[{"key":"174_CR1","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1093\/bib\/bbs064","volume":"15","author":"W Wruck","year":"2014","unstructured":"Wruck W, Peuker M, Regenbrecht CR. Data management strategies for multinational large-scale systems biology projects. Brief Bioinform. 2014;15:65\u201378.","journal-title":"Brief Bioinform"},{"key":"174_CR2","doi-asserted-by":"publisher","first-page":"D553","DOI":"10.1093\/nar\/gki056","volume":"33","author":"H Parkinson","year":"2005","unstructured":"Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S, Coulson R, et al. ArrayExpress\u2013a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 2005;33:D553\u2013555.","journal-title":"Nucleic Acids Res"},{"key":"174_CR3","first-page":"Unit 25 24","volume":"Chapter 25","author":"JA Vizcaino","year":"2010","unstructured":"Vizcaino JA, Reisinger F, Cote R, Martens L. PRIDE: Data submission and analysis. Curr Protoc Protein Sci. 2010;Chapter 25:Unit 25 24.","journal-title":"Curr Protoc Protein Sci"},{"key":"174_CR4","doi-asserted-by":"publisher","first-page":"2354","DOI":"10.1093\/bioinformatics\/btq415","volume":"26","author":"P Rocca-Serra","year":"2010","unstructured":"Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C, Begley K, et al. ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics. 2010;26:2354\u20136.","journal-title":"Bioinformatics"},{"key":"174_CR5","doi-asserted-by":"crossref","unstructured":"Data producers deserve citation credit. Nat Genet 2009, 41:1045.","DOI":"10.1038\/ng1009-1045"},{"key":"174_CR6","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1038\/ng1201-365","volume":"29","author":"A Brazma","year":"2001","unstructured":"Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001;29:365\u201371.","journal-title":"Nat Genet"},{"key":"174_CR7","doi-asserted-by":"publisher","first-page":"765","DOI":"10.1007\/978-1-62703-631-3_53","volume":"1072","author":"S Martinez-Bartolome","year":"2014","unstructured":"Martinez-Bartolome S, Binz PA, Albar JP. The Minimal Information about a Proteomics Experiment (MIAPE) from the Proteomics Standards Initiative. Methods Mol Biol. 2014;1072:765\u201380.","journal-title":"Methods Mol Biol"},{"key":"174_CR8","doi-asserted-by":"publisher","first-page":"1509","DOI":"10.1038\/nbt1156","volume":"23","author":"N Novere Le","year":"2005","unstructured":"Le Novere N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, et al. Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol. 2005;23:1509\u201315.","journal-title":"Nat Biotechnol"},{"key":"174_CR9","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1016\/B978-0-12-385118-5.00029-3","volume":"500","author":"K Wolstencroft","year":"2011","unstructured":"Wolstencroft K, Owen S, du Preez F, Krebs O, Mueller W, Goble C, et al. The SEEK: a platform for sharing data and models in systems biology. Methods Enzymol. 2011;500:629\u201355.","journal-title":"Methods Enzymol"},{"key":"174_CR10","doi-asserted-by":"publisher","first-page":"2021","DOI":"10.1093\/bioinformatics\/btr312","volume":"27","author":"K Wolstencroft","year":"2011","unstructured":"Wolstencroft K, Owen S, Horridge M, Krebs O, Mueller W, Snoep JL, et al. RightField: embedding ontology annotation in spreadsheets. Bioinformatics. 2011;27:2021\u20132.","journal-title":"Bioinformatics"},{"key":"174_CR11","doi-asserted-by":"publisher","first-page":"2143","DOI":"10.1093\/bioinformatics\/bth200","volume":"20","author":"BG Olivier","year":"2004","unstructured":"Olivier BG, Snoep JL. Web-based kinetic modelling using JWS Online. Bioinformatics. 2004;20:2143\u20134.","journal-title":"Bioinformatics"},{"key":"174_CR12","doi-asserted-by":"publisher","first-page":"D991","DOI":"10.1093\/nar\/gks1193","volume":"41","author":"T Barrett","year":"2013","unstructured":"Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, et al. NCBI GEO: archive for functional genomics data sets\u2013update. Nucleic Acids Res. 2013;41:D991\u2013995.","journal-title":"Nucleic Acids Res"},{"key":"174_CR13","doi-asserted-by":"publisher","first-page":"D542","DOI":"10.1093\/nar\/gku1181","volume":"43","author":"V Chelliah","year":"2015","unstructured":"Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M, et al. BioModels: ten-year anniversary. Nucleic Acids Res. 2015;43:D542\u2013548.","journal-title":"Nucleic Acids Res"},{"key":"174_CR14","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","volume":"19","author":"M Hucka","year":"2003","unstructured":"Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003;19:524\u201331.","journal-title":"Bioinformatics"},{"key":"174_CR15","first-page":"212","volume-title":"The Semantic Web (ISWC); Sydney, Australia","author":"W Katherine","year":"2013","unstructured":"Katherine W, Stuart O, Olga K, Wolfgang M, Quyen N, Snoep JL, et al. Semantic Data and Models Sharing in Systems Biology: The Just Enough Results Model and the SEEK Platform. In: The Semantic Web (ISWC); Sydney, Australia. Berlin Heidelberg: Springer; 2013. p. 212\u201327."},{"key":"174_CR16","doi-asserted-by":"publisher","first-page":"D344","DOI":"10.1093\/nar\/gkm791","volume":"36","author":"K Degtyarenko","year":"2008","unstructured":"Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, et al. ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 2008;36:D344\u2013350.","journal-title":"Nucleic Acids Res"},{"key":"174_CR17","doi-asserted-by":"publisher","first-page":"1338","DOI":"10.1093\/bioinformatics\/btt765","volume":"30","author":"S Jupp","year":"2014","unstructured":"Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L, et al. The EBI RDF platform: linked open data for the life sciences. Bioinformatics. 2014;30:1338\u20139.","journal-title":"Bioinformatics"},{"key":"174_CR18","doi-asserted-by":"publisher","first-page":"706","DOI":"10.1016\/j.jbi.2008.03.004","volume":"41","author":"F Belleau","year":"2008","unstructured":"Belleau F, Nolin MA, Tourigny N, Rigault P, Morissette J. Bio2RDF: towards a mashup to build bioinformatics knowledge systems. J Biomed Inform. 2008;41:706\u201316.","journal-title":"J Biomed Inform"},{"key":"174_CR19","doi-asserted-by":"publisher","first-page":"S4","DOI":"10.1186\/1471-2105-15-S14-S4","volume":"15 Suppl 14","author":"A Gonzalez-Beltran","year":"2014","unstructured":"Gonzalez-Beltran A, Maguire E, Sansone SA, Rocca-Serra P. linkedISA: semantic representation of ISA-Tab experimental metadata. BMC Bioinformatics. 2014;15 Suppl 14:S4.","journal-title":"BMC Bioinformatics"},{"key":"174_CR20","doi-asserted-by":"publisher","first-page":"W541","DOI":"10.1093\/nar\/gkr469","volume":"39","author":"PL Whetzel","year":"2011","unstructured":"Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, et al. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011;39:W541\u2013545.","journal-title":"Nucleic Acids Res"},{"key":"174_CR21","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1093\/bioinformatics\/btp642","volume":"26","author":"F Krause","year":"2010","unstructured":"Krause F, Uhlendorf J, Lubitz T, Schulz M, Klipp E, Liebermeister W. Annotation and merging of SBML models with semanticSBML. Bioinformatics. 2010;26:421\u20132.","journal-title":"Bioinformatics"},{"key":"174_CR22","doi-asserted-by":"publisher","first-page":"735","DOI":"10.1038\/nbt.1558","volume":"27","author":"N Novere Le","year":"2009","unstructured":"Le Novere N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, et al. The Systems Biology Graphical Notation. Nat Biotechnol. 2009;27:735\u201341.","journal-title":"Nat Biotechnol"},{"key":"174_CR23","doi-asserted-by":"publisher","first-page":"2347","DOI":"10.1093\/bioinformatics\/btq430","volume":"26","author":"CT Lopes","year":"2010","unstructured":"Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD. Cytoscape Web: an interactive web-based network browser. Bioinformatics. 2010;26:2347\u20138.","journal-title":"Bioinformatics"},{"key":"174_CR24","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1186\/1752-0509-5-198","volume":"5","author":"D Waltemath","year":"2011","unstructured":"Waltemath D, Adams R, Bergmann FT, Hucka M, Kolpakov F, Miller AK, et al. Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language. BMC Syst Biol. 2011;5:198.","journal-title":"BMC Syst Biol"},{"key":"174_CR25","doi-asserted-by":"publisher","first-page":"D781","DOI":"10.1093\/nar\/gks1004","volume":"41","author":"K Haug","year":"2013","unstructured":"Haug K, Salek RM, Conesa P, Hastings J, de Matos P, Rijnbeek M, et al. MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data. Nucleic Acids Res. 2013;41:D781\u2013786.","journal-title":"Nucleic Acids Res"},{"key":"174_CR26","doi-asserted-by":"publisher","first-page":"468","DOI":"10.1186\/1471-2105-12-468","volume":"12","author":"A Bauch","year":"2011","unstructured":"Bauch A, Adamczyk I, Buczek P, Elmer FJ, Enimanev K, Glyzewski P, et al. openBIS: a flexible framework for managing and analyzing complex data in biology research. BMC Bioinformatics. 2011;12:468.","journal-title":"BMC Bioinformatics"},{"key":"174_CR27","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1186\/1471-2105-13-85","volume":"13","author":"F Dreher","year":"2012","unstructured":"Dreher F, Kreitler T, Hardt C, Kamburov A, Yildirimman R, Schellander K, et al. DIPSBC--data integration platform for systems biology collaborations. BMC Bioinformatics. 2012;13:85.","journal-title":"BMC Bioinformatics"},{"key":"174_CR28","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1186\/1471-2105-13-311","volume":"13","author":"SC Tilton","year":"2012","unstructured":"Tilton SC, Tal TL, Scroggins SM, Franzosa JA, Peterson ES, Tanguay RL, et al. Bioinformatics Resource Manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools. BMC Bioinformatics. 2012;13:311.","journal-title":"BMC Bioinformatics"},{"key":"174_CR29","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1038\/ng.1054","volume":"44","author":"SA Sansone","year":"2012","unstructured":"Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, et al. Toward interoperable bioscience data. Nat Genet. 2012;44:121\u20136.","journal-title":"Nat Genet"},{"key":"174_CR30","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1186\/1471-2105-7-176","volume":"7","author":"PT Shannon","year":"2006","unstructured":"Shannon PT, Reiss DJ, Bonneau R, Baliga NS. The Gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics. 2006;7:176.","journal-title":"BMC Bioinformatics"},{"key":"174_CR31","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1186\/1471-2105-12-71","volume":"12","author":"EK Nelson","year":"2011","unstructured":"Nelson EK, Piehler B, Eckels J, Rauch A, Bellew M, Hussey P, et al. LabKey Server: an open source platform for scientific data integration, analysis and collaboration. BMC Bioinformatics. 2011;12:71.","journal-title":"BMC Bioinformatics"},{"key":"174_CR32","doi-asserted-by":"publisher","first-page":"4666","DOI":"10.1111\/febs.12438","volume":"280","author":"T Kouril","year":"2013","unstructured":"Kouril T, Esser D, Kort J, Westerhoff HV, Siebers B, Snoep JL. Intermediate instability at high temperature leads to low pathway efficiency for an in vitro reconstituted system of gluconeogenesis in Sulfolobus solfataricus. FEBS J. 2013;280:4666\u201380.","journal-title":"FEBS J"},{"key":"174_CR33","doi-asserted-by":"publisher","first-page":"D790","DOI":"10.1093\/nar\/gkr1046","volume":"40","author":"U Wittig","year":"2012","unstructured":"Wittig U, Kania R, Golebiewski M, Rey M, Shi L, Jong L, et al. SABIO-RK\u2013database for biochemical reaction kinetics. Nucleic Acids Res. 2012;40:D790\u2013796.","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12918-015-0174-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-015-0174-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-015-0174-y","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-015-0174-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,2,3]],"date-time":"2020-02-03T14:28:11Z","timestamp":1580740091000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/s12918-015-0174-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,7,11]]},"references-count":33,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["174"],"URL":"https:\/\/doi.org\/10.1186\/s12918-015-0174-y","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,7,11]]},"assertion":[{"value":"2 March 2015","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 June 2015","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 July 2015","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"33"}}