{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T16:07:01Z","timestamp":1785859621479,"version":"3.56.0"},"reference-count":43,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Modern data generation techniques used in distributed systems biology research projects often create datasets of enormous size and diversity. We argue that in order to overcome the challenge of managing those large quantitative datasets and maximise the biological information extracted from them, a sound information system is required. Ease of integration with data analysis pipelines and other computational tools is a key requirement for it.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We have developed openBIS, an open source software framework for constructing user-friendly, scalable and powerful information systems for data and metadata acquired in biological experiments. openBIS enables users to collect, integrate, share, publish data and to connect to data processing pipelines. This framework can be extended and has been customized for different data types acquired by a range of technologies.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>openBIS is currently being used by several SystemsX.ch and EU projects applying mass spectrometric measurements of metabolites and proteins, High Content Screening, or Next Generation Sequencing technologies. The attributes that make it interesting to a large research community involved in systems biology projects include versatility, simplicity in deployment, scalability to very large data, flexibility to handle any biological data type and extensibility to the needs of any research domain.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-468","type":"journal-article","created":{"date-parts":[[2011,12,8]],"date-time":"2011-12-08T20:33:29Z","timestamp":1323376409000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":135,"title":["openBIS: a flexible framework for managing and analyzing complex data in biology research"],"prefix":"10.1186","volume":"12","author":[{"given":"Angela","family":"Bauch","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Izabela","family":"Adamczyk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Piotr","family":"Buczek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Franz-Josef","family":"Elmer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaloyan","family":"Enimanev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pawel","family":"Glyzewski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuel","family":"Kohler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomasz","family":"Pylak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Quandt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chandrasekhar","family":"Ramakrishnan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian","family":"Beisel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lars","family":"Malmstr\u00f6m","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruedi","family":"Aebersold","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bernd","family":"Rinn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2011,12,8]]},"reference":[{"key":"5019_CR1","first-page":"678","volume-title":"Nat Rev Genet","author":"LD Stein","year":"2008","unstructured":"Stein LD: Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges. Nat Rev Genet 2008, 678\u201388."},{"key":"5019_CR2","first-page":"1225","volume-title":"Nat Immunol","author":"D Chaussabel","year":"2009","unstructured":"Chaussabel D, Ueno H, Banchereau J, Quinn C: Data Management: It Starts at the Bench. Nat Immunol 2009, 1225\u20131227."},{"key":"5019_CR3","first-page":"228","volume-title":"Drug Discov Today","author":"H Rauwerda","year":"2006","unstructured":"Rauwerda H, Roos M, Hertzberger BO, Breit TM: The promise of a virtual lab in drug discovery. Drug Discov Today 2006, 228\u201336."},{"key":"5019_CR4","first-page":"728","volume-title":"Science","author":"SD Kahn","year":"2011","unstructured":"Kahn SD: On the future of genomics data. Science 2011, 728\u20139."},{"key":"5019_CR5","first-page":"151","volume-title":"BMC Bioinformatics","author":"A Gattiker","year":"2009","unstructured":"Gattiker A, Hermida L, Liechti R, Xenarios I, Collin O, Rougemont J, Primig M: MIMAS 3.0 is a Multiomics Information Management and Annotation System. BMC Bioinformatics 2009, 151."},{"key":"5019_CR6","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1186\/1471-2105-9-379","volume":"9","author":"C Tomlinson","year":"2008","unstructured":"Tomlinson C, Thimma M, Alexandrakis S, Castillo T, Dennis JL, Brooks A, Bradley T, Turnbull C, Blaveri E, Barton G, et al.: MiMiR - an integrated platform for microarray data sharing, mining and analysis. BMC Bioinformatics 2008, 9: 379. 10.1186\/1471-2105-9-379","journal-title":"BMC Bioinformatics"},{"key":"5019_CR7","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1186\/1471-2105-11-455","volume":"11","author":"DA Nix","year":"2010","unstructured":"Nix DA, Di Sera TL, Dalley BK, Milash BA, Cundick RM, Quinn KS, Courdy SJ: Next generation tools for genomic data generation, distribution, and visualization. BMC Bioinformatics 2010, 11: 455. 10.1186\/1471-2105-11-455","journal-title":"BMC Bioinformatics"},{"key":"5019_CR8","first-page":"610","volume-title":"BMC Bioinformatics","author":"S Kozhenkov","year":"2010","unstructured":"Kozhenkov S, Dubinina Y, Sedova M, Gupta A, Ponomarenko J, Baitaluk M: BiologicalNetworks 2.0 an integrative view of genome biology data. BMC Bioinformatics 2010, 610."},{"key":"5019_CR9","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1021\/pr0503533","volume":"5","author":"A Rauch","year":"2006","unstructured":"Rauch A, Bellew M, Eng J, Fitzgibbon M, Holzman T, Hussey P, Igra M, Maclean B, Lin CW, Detter A, Fang R, Faca V, Gafken P, Zhang H, Whiteaker J, States D, Hanash S, Paulovich A, McIntosh MW: Computational Proteomics Analysis System (CPAS): An Extensible, Open-Source Analytic System for Evaluating and Publishing Proteomic Data and High throughput Biological Experiments. J Proteome Research 2006, 5: 112\u2013121. 10.1021\/pr0503533","journal-title":"J Proteome Research"},{"key":"5019_CR10","doi-asserted-by":"publisher","first-page":"1783","DOI":"10.1002\/pmic.200500500","volume":"6","author":"GR Kiebel","year":"2006","unstructured":"Kiebel GR, Auberry KJ, Jaitly N, Clark DA, Monroe ME, Peterson ES, Tolic N, Anderson GA, Smith RD: PRISM: A data management system for high-throughput proteomics. Proteomics 2006, 6: 1783\u20131790. 10.1002\/pmic.200500500","journal-title":"Proteomics"},{"key":"5019_CR11","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1186\/1471-2105-7-158","volume":"7","author":"L Malmstr\u00f6m","year":"2006","unstructured":"Malmstr\u00f6m L, Marko-Varga G, Westergren-Thorsson G, Laurell T, Malmstr\u00f6m J: 2DDB - a bioinformatics solution for analysis of quantitative proteomics data. BMC Bioinformatics 2006, 7: 158. 10.1186\/1471-2105-7-158","journal-title":"BMC Bioinformatics"},{"key":"5019_CR12","doi-asserted-by":"publisher","first-page":"1131","DOI":"10.1093\/bioinformatics\/btq081","volume":"26","author":"DC Trudgian","year":"2010","unstructured":"Trudgian DC, Thomas B, McGowan SJ, Kessler BM, Salek M, Acuto O: CPFP: a central proteomics facilities pipeline. Bioinformatics 2010, 26: 1131\u20132. 10.1093\/bioinformatics\/btq081","journal-title":"Bioinformatics"},{"key":"5019_CR13","doi-asserted-by":"publisher","first-page":"2719","DOI":"10.1002\/pmic.201000075","volume":"10","author":"C Ubaida Mohien","year":"2010","unstructured":"Ubaida Mohien C, Hartler J, Breitwieser F, Rix U, Remsing Rix L, Winter GE, Thallinger GG, Bennett KL, Superti-Furga G, Trajanoski Z, Colinge J: MASPECTRAS 2: An integration and analysis platform for proteomic data. Proteomics 2010, 10: 2719\u201322. 10.1002\/pmic.201000075","journal-title":"Proteomics"},{"key":"5019_CR14","doi-asserted-by":"publisher","first-page":"1015","DOI":"10.1038\/nbt1010-1015","volume":"10","author":"G Liu","year":"2010","unstructured":"Liu G, Zhang J, Larsen B, Stark C, Breitkreutz A, Lin ZY, Breitkreutz BJ, Ding Y, Colwill K, Pasculescu A, Pawson T, Wrana JL, Nesvizhskii AI, Raught B, Tyers M, Gingras AC: ProHits: integrated software for mass spectrometry-based interaction proteomics. Nat Biotechnol 2010, 10: 1015\u20137.","journal-title":"Nat Biotechnol"},{"key":"5019_CR15","doi-asserted-by":"publisher","first-page":"R86","DOI":"10.1186\/gb-2010-11-8-r86","volume":"11","author":"J Goecks","year":"2010","unstructured":"Goecks J, Nekrutenko A, Taylor J, Galaxy Team: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010, 11: R86. 10.1186\/gb-2010-11-8-r86","journal-title":"Genome Biol"},{"key":"5019_CR16","unstructured":"KNIME[http:\/\/www.knime.org\/]"},{"key":"5019_CR17","doi-asserted-by":"publisher","first-page":"3045","DOI":"10.1093\/bioinformatics\/bth361","volume":"20","author":"T Oinn","year":"2004","unstructured":"Oinn T, Addis M, Ferris J, Marvin D, Senger M, Greenwood M, Carver T, Glover K, Pocock MR, Wipat A, Li P: Taverna, an exemplar platform for integrating bioinformatics workflows across loosely coupled sites and thechnologies that share common semantics. Bioinformatics 2004, 20: 3045\u20133054. 10.1093\/bioinformatics\/bth361","journal-title":"Bioinformatics"},{"key":"5019_CR18","volume-title":"Proceedings of the The Future of Grid Data Environments","author":"I Altintas","year":"2004","unstructured":"Altintas I, Berkley C, Jaeger E, Jones M, Lud\u00e4scher B, Mock S: Kepler: An Extensible System for Design and Execution of Scientific Workflows. Proceedings of the The Future of Grid Data Environments 2004. Global Grid Forum 10 Global Grid Forum 10"},{"key":"5019_CR19","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1007\/s10723-005-9012-6","volume":"3","author":"P Kacsuk","year":"2005","unstructured":"Kacsuk P, Sipos G: Multi-Grid, Multi-User Workflows in the P-GRADE Grid Portal. J Grid Comp 2005, 3: 221\u2013238. 10.1007\/s10723-005-9012-6","journal-title":"J Grid Comp"},{"key":"5019_CR20","doi-asserted-by":"publisher","first-page":"e191","DOI":"10.1093\/bioinformatics\/btl299","volume":"23","author":"O Kohlbacher","year":"2007","unstructured":"Kohlbacher O, Reinert K, Gr\u00f6pl C, Lange E, Pfeifer N, Schulz-Trieglaff O, Sturm M: TOPP-the OpenMS proteomics pipeline. Bioinformatics 2007, 23: e191\u20137. 10.1093\/bioinformatics\/btl299","journal-title":"Bioinformatics"},{"key":"5019_CR21","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1109\/5992.764215","volume":"3","author":"LD Stein","year":"1999","unstructured":"Stein LD, Thierry-Mieg J: AceDB: a genome database management system. Computing in Science & Engineering 1999, 3: 44\u201352.","journal-title":"Computing in Science & Engineering"},{"key":"5019_CR22","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1186\/1471-2105-7-286","volume":"7","author":"B Marzolf","year":"2006","unstructured":"Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T: SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 2006, 7: 286. 10.1186\/1471-2105-7-286","journal-title":"BMC Bioinformatics"},{"key":"5019_CR23","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1515\/jib-2011-159","volume":"8","author":"C T\u00fcrker","year":"2011","unstructured":"T\u00fcrker C, Akal F, Schlapbach R: Life sciences data and application integration with B-fabric. J Integr Bioinform 2011, 8: 159.","journal-title":"J Integr Bioinform"},{"key":"5019_CR24","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, Snoep JL: The SEEK: a platform for sharing data and models in systems biology. Methods Enzymol 2011, 500: 629\u201355.","journal-title":"Methods Enzymol"},{"key":"5019_CR25","first-page":"34","volume":"4","author":"K Kozak","year":"2010","unstructured":"Kozak K, Bauch A, Csucs G, Pylak T, Rinn B: Towards a comprehensive open source platform for management and analysis of High Content Screening data. Eur Pharmaceut Rev 2010, 4: 34\u201339.","journal-title":"Eur Pharmaceut Rev"},{"key":"5019_CR26","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1002\/bs.3830180202","volume":"18","author":"RB Glassman","year":"1973","unstructured":"Glassman RB: Persistence and loose coupling in living systems. Behavioral Science 1973, 18: 83\u201398. 10.1002\/bs.3830180202","journal-title":"Behavioral Science"},{"key":"5019_CR27","volume-title":"McGraw-Hill Higher Education","author":"RS Pressman","year":"1982","unstructured":"Pressman RS: Software Engineering: A Practitioner's Approach. McGraw-Hill Higher Education 1982. ISBN 0\u2013071\u201326782\u20134 ISBN 0-071-26782-4"},{"issue":"11-12","key":"5019_CR28","doi-asserted-by":"publisher","first-page":"769","DOI":"10.1016\/j.ijmedinf.2006.09.023","volume":"76","author":"V Donu","year":"2007","unstructured":"Donu V, Nadkarni P: Guidelines for the effective use of entity-attribute-value modeling for biomedical databases. Int J Med Inform 2007, 76(11\u201312):769\u2013779. 10.1016\/j.ijmedinf.2006.09.023","journal-title":"Int J Med Inform"},{"issue":"6","key":"5019_CR29","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1145\/362384.362685","volume":"13","author":"EF Codd","year":"1970","unstructured":"Codd EF: A Relational Model of Data for Large Shared Data Banks. Comm ACM 1970, 13(6):377\u2013387. 10.1145\/362384.362685","journal-title":"Comm ACM"},{"key":"5019_CR30","unstructured":"CIFEX[https:\/\/wiki-bsse.ethz.ch\/display\/CFX\/Home]"},{"key":"5019_CR31","unstructured":"Atlassian[http:\/\/www.atlassian.com\/software\/crowd]"},{"key":"5019_CR32","unstructured":"SRF[http:\/\/srf.sourceforge.net]"},{"key":"5019_CR33","unstructured":"Demo instance[http:\/\/openbis-demo.ethz.ch]"},{"key":"5019_CR34","first-page":"216","volume-title":"Genome Res","author":"D Enderle","year":"2011","unstructured":"Enderle D, Beisel C, Stadler MB, Gerstung M, Athri P, Paro R: Polycomb preferentially targets stalled promoters of coding and noncoding trascripts. Genome Res 2011, (2):216\u201326."},{"key":"5019_CR35","first-page":"123","volume-title":"Nat Rev Genet","author":"C Beisel","year":"2011","unstructured":"Beisel C, Paro R: Silencing chromatin: comparing modes and mechanisms. Nat Rev Genet 2011, (2):123\u201335."},{"key":"5019_CR36","unstructured":"UCSC Genome Browser[http:\/\/genome.ucsc.edu\/cgi-bin\/hgGateway]"},{"key":"5019_CR37","doi-asserted-by":"publisher","first-page":"1459","DOI":"10.1038\/nbt1031","volume":"22","author":"PGA Pedrioli","year":"2004","unstructured":"Pedrioli PGA, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK Jr, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R: A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotech 2004, 22: 1459\u20131466. 10.1038\/nbt1031","journal-title":"Nat Biotech"},{"key":"5019_CR38","volume-title":"J Biol Chem","author":"J Malmstrom","year":"2011","unstructured":"Malmstrom J, Karlsson C, Nordenfelt P, Ossola R, Weisser H, Quandt A, Hansson K, Aebersold R, Malmstrom L, Bjorck L: Streptococcus pyogenes in human plasma: adaptive mechanisms analyzed by mass spectrometry based proteomics. J Biol Chem 2011, in press."},{"key":"5019_CR39","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1128\/iai.65.1.64-71.1997","volume":"65","author":"AE Moses","year":"1997","unstructured":"Moses AE: Relative Contributions of Hyaluronic Acid Capsule and M Protein to Virulence in a Mucoid Strain of the Group A Streptococcus. Infect Immun 1997, 65: 64\u201371.","journal-title":"Infect Immun"},{"key":"5019_CR40","unstructured":"openBIS Documentation and Download Site[https:\/\/wiki-bsse.ethz.ch\/display\/bis\/Home]"},{"key":"5019_CR41","unstructured":"GEO[http:\/\/www.ncbi.nlm.nih.gov\/geo\/]"},{"key":"5019_CR42","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/msb4100024","volume":"1","author":"A Keller","year":"2005","unstructured":"Keller A, Eng J, Zhang N, Li XJ, Aebersold R: A uniform proteomics MS\/MS analysis platform utilizing open XML file formats. Mol Syst Biol 2005, 1: 1\u20138.","journal-title":"Mol Syst Biol"},{"key":"5019_CR43","unstructured":"PeptideAtlas[http:\/\/www.peptideatlas.org]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-468.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T18:19:03Z","timestamp":1630520343000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-468"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,12]]},"references-count":43,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["5019"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-468","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,12]]},"assertion":[{"value":"6 September 2011","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 December 2011","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 December 2011","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"468"}}