{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T16:39:29Z","timestamp":1761237569329},"reference-count":30,"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":[[2008,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Despite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-using the large amount of data generated locally or internationally. Additionally, it is recognised that inconsistent and low quality experimental annotation in public data repositories significantly compromises the re-use of microarray data for meta-analysis. MiMiR, the <jats:bold>Mi<\/jats:bold> croarray data <jats:bold>Mi<\/jats:bold> ning <jats:bold>R<\/jats:bold> esource was designed to tackle some of these limitations and challenges. Here we present new software components and enhancements to the original infrastructure that increase accessibility, utility and opportunities for large scale mining of experimental and clinical data.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>A user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>The new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-9-379","type":"journal-article","created":{"date-parts":[[2008,9,18]],"date-time":"2008-09-18T18:13:34Z","timestamp":1221761614000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["MiMiR \u2013 an integrated platform for microarray data sharing, mining and analysis"],"prefix":"10.1186","volume":"9","author":[{"given":"Chris","family":"Tomlinson","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manjula","family":"Thimma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stelios","family":"Alexandrakis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tito","family":"Castillo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jayne L","family":"Dennis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anthony","family":"Brooks","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Bradley","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carly","family":"Turnbull","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ekaterini","family":"Blaveri","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Geraint","family":"Barton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Norie","family":"Chiba","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Klio","family":"Maratou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pat","family":"Soutter","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tim","family":"Aitman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laurence","family":"Game","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,9,18]]},"reference":[{"issue":"11","key":"2364_CR1","doi-asserted-by":"publisher","first-page":"1322","DOI":"10.1038\/nbt1106-1322","volume":"24","author":"O Larsson","year":"2006","unstructured":"Larsson O, Sandberg R: Lack of correct data format and comparability limits future integrative microarray research. Nat Biotechnol 2006, 24(11):1322\u20131323. 10.1038\/nbt1106-1322","journal-title":"Nat Biotechnol"},{"key":"2364_CR2","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1002\/cfg.234","volume":"4","author":"C Stoeckert","year":"2003","unstructured":"Stoeckert C, Parkinson H: The MGED Ontology: a framework for describing functional genomics experiments. Comparitive and Functional Genomics 2003, 4: 127\u2013132. 10.1002\/cfg.234","journal-title":"Comparitive and Functional Genomics"},{"issue":"7","key":"2364_CR3","doi-asserted-by":"publisher","first-page":"866","DOI":"10.1093\/bioinformatics\/btl005","volume":"22","author":"PL Whetzel","year":"2006","unstructured":"Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, et al.: The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics 2006, 22(7):866\u2013873. 10.1093\/bioinformatics\/btl005","journal-title":"Bioinformatics"},{"issue":"9","key":"2364_CR4","doi-asserted-by":"publisher","first-page":"RESEARCH0046","DOI":"10.1186\/gb-2002-3-9-research0046","volume":"3","author":"PT Spellman","year":"2002","unstructured":"Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, et al.: Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol 2002, 3(9):RESEARCH0046. 10.1186\/gb-2002-3-9-research0046","journal-title":"Genome Biol"},{"issue":"4","key":"2364_CR5","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, Aach J, Ansorge W, Ball CA, Causton HC, et al.: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 2001, 29(4):365\u2013371. 10.1038\/ng1201-365","journal-title":"Nat Genet"},{"issue":"4","key":"2364_CR6","doi-asserted-by":"publisher","first-page":"657","DOI":"10.1016\/j.cell.2006.11.005","volume":"127","author":"E Strauss","year":"2006","unstructured":"Strauss E: Arrays of hope. Cell 2006, 127(4):657\u2013659. 10.1016\/j.cell.2006.11.005","journal-title":"Cell"},{"key":"2364_CR7","doi-asserted-by":"publisher","first-page":"D760","DOI":"10.1093\/nar\/gkl887","volume-title":"Nucleic Acids Res","author":"T Barrett","year":"2007","unstructured":"Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R: NCBI GEO: mining tens of millions of expression profiles\u2013database and tools update. Nucleic Acids Res 2007, (35 Database):D760\u2013765. 10.1093\/nar\/gkl887"},{"key":"2364_CR8","doi-asserted-by":"publisher","first-page":"D747","DOI":"10.1093\/nar\/gkl995","volume-title":"Nucleic Acids Res","author":"H Parkinson","year":"2007","unstructured":"Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, et al.: ArrayExpress\u2013a public database of microarray experiments and gene expression profiles. Nucleic Acids Res 2007, (35 Database):D747\u2013750. 10.1093\/nar\/gkl995"},{"key":"2364_CR9","doi-asserted-by":"publisher","first-page":"D618","DOI":"10.1093\/nar\/gkl1003","volume-title":"Nucleic Acids Res","author":"CM Smith","year":"2007","unstructured":"Smith CM, Finger JH, Hayamizu TF, McCright IJ, Eppig JT, Kadin JA, Richardson JE, Ringwald M: The mouse Gene Expression Database (GXD): 2007 update. Nucleic Acids Res 2007, (35 Database):D618\u2013623. 10.1093\/nar\/gkl1003"},{"issue":"8","key":"2364_CR10","doi-asserted-by":"publisher","first-page":"SOFTWARE0003","DOI":"10.1186\/gb-2002-3-8-software0003","volume":"3","author":"LH Saal","year":"2002","unstructured":"Saal LH, Troein C, Vallon-Christersson J, Gruvberger S, Borg A, Peterson C: BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. Genome Biol 2002, 3(8):SOFTWARE0003. 10.1186\/gb-2002-3-8-software0003","journal-title":"Genome Biol"},{"issue":"1","key":"2364_CR11","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1093\/nar\/gkg078","volume":"31","author":"J Gollub","year":"2003","unstructured":"Gollub J, Ball CA, Binkley G, Demeter J, Finkelstein DB, Hebert JM, Hernandez-Boussard T, Jin H, Kaloper M, Matese JC, et al.: The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res 2003, 31(1):94\u201396. 10.1093\/nar\/gkg078","journal-title":"Nucleic Acids Res"},{"key":"2364_CR12","doi-asserted-by":"publisher","first-page":"D751","DOI":"10.1093\/nar\/gkl748","volume-title":"Nucleic Acids Res","author":"JM Mazzarelli","year":"2007","unstructured":"Mazzarelli JM, Brestelli J, Gorski RK, Liu J, Manduchi E, Pinney DF, Schug J, White P, Kaestner KH, Stoeckert CJ Jr: EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes. Nucleic Acids Res 2007, (35 Database):D751\u2013755. 10.1093\/nar\/gkl748"},{"key":"2364_CR13","doi-asserted-by":"publisher","first-page":"D756","DOI":"10.1093\/nar\/gkl798","volume-title":"Nucleic Acids Res","author":"F Pan","year":"2007","unstructured":"Pan F, Chiu CH, Pulapura S, Mehan MR, Nunez-Iglesias J, Zhang K, Kamath K, Waterman MS, Finch CE, Zhou XJ: Gene Aging Nexus: a web database and data mining platform for microarray data on aging. Nucleic Acids Res 2007, (35 Database):D756\u2013759. 10.1093\/nar\/gkl798"},{"issue":"Suppl 1","key":"2364_CR14","doi-asserted-by":"publisher","first-page":"S21","DOI":"10.1186\/1471-2105-8-S1-S21","volume":"8","author":"A Splendiani","year":"2007","unstructured":"Splendiani A, Brandizi M, Even G, Beretta O, Pavelka N, Pelizzola M, Mayhaus M, Foti M, Mauri G, Ricciardi-Castagnoli P: The genopolis microarray database. BMC Bioinformatics 2007, 8(Suppl 1):S21. 10.1186\/1471-2105-8-S1-S21","journal-title":"BMC Bioinformatics"},{"key":"2364_CR15","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":"2364_CR16","doi-asserted-by":"publisher","first-page":"D766","DOI":"10.1093\/nar\/gkl1019","volume-title":"Nucleic Acids Res","author":"J Demeter","year":"2007","unstructured":"Demeter J, Beauheim C, Gollub J, Hernandez-Boussard T, Jin H, Maier D, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, et al.: The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res 2007, (35 Database):D766\u2013770. 10.1093\/nar\/gkl1019"},{"issue":"8","key":"2364_CR17","doi-asserted-by":"publisher","first-page":"1024","DOI":"10.1093\/bioinformatics\/btl036","volume":"22","author":"A Ameur","year":"2006","unstructured":"Ameur A, Yankovski V, Enroth S, Spjuth O, Komorowski J: The LCB Data Warehouse. Bioinformatics 2006, 22(8):1024\u20131026. 10.1093\/bioinformatics\/btl036","journal-title":"Bioinformatics"},{"issue":"10","key":"2364_CR18","doi-asserted-by":"publisher","first-page":"1304","DOI":"10.1093\/bioinformatics\/btm106","volume":"23","author":"K Le Brigand","year":"2007","unstructured":"Le Brigand K, Barbry P: Mediante: a web-based microarray data manager. Bioinformatics 2007, 23(10):1304\u20131306. 10.1093\/bioinformatics\/btm106","journal-title":"Bioinformatics"},{"key":"2364_CR19","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1186\/1471-2105-6-268","volume":"6","author":"M Navarange","year":"2005","unstructured":"Navarange M, Game L, Fowler D, Wadekar V, Banks H, Cooley N, Rahman F, Hinshelwood J, Broderick P, Causton HC: MiMiR: a comprehensive solution for storage, annotation and exchange of microarray data. BMC Bioinformatics 2005, 6: 268. 10.1186\/1471-2105-6-268","journal-title":"BMC Bioinformatics"},{"key":"2364_CR20","volume-title":"BMC Bioinformatics","author":"G Barton","year":"2008","unstructured":"Barton G, Saleem A, Krznaric M, Abbott J, MJ S, Tiwari B, Aitman T, Game LJMS, Huang Y, et al.: EMAAS: An extensible grid-based portal for microarray data analysis and management. BMC Bioinformatics 2008, in press."},{"key":"2364_CR21","first-page":"32","volume-title":"Supplement to Nature Genetics","author":"The Chipping Forecast II","year":"2002","unstructured":"The Chipping Forecast II: Supplement to Nature Genetics. 2002, 32."},{"key":"2364_CR22","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1186\/1471-2105-8-426","volume":"8","author":"BT Sherman","year":"2007","unstructured":"Sherman BT, Huang da W, Tan Q, Guo Y, Bour S, Liu D, Stephens R, Baseler MW, Lane HC, Lempicki RA: DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. BMC Bioinformatics 2007, 8: 426. 10.1186\/1471-2105-8-426","journal-title":"BMC Bioinformatics"},{"issue":"6","key":"2364_CR23","doi-asserted-by":"publisher","first-page":"R112","DOI":"10.1186\/gb-2007-8-6-r112","volume":"8","author":"A Day","year":"2007","unstructured":"Day A, Carlson MR, Dong J, O'Connor BD, Nelson SF: Celsius: a community resource for Affymetrix microarray data. Genome Biol 2007, 8(6):R112. 10.1186\/gb-2007-8-6-r112","journal-title":"Genome Biol"},{"issue":"1","key":"2364_CR24","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1093\/nar\/gkg050","volume":"31","author":"M Safran","year":"2003","unstructured":"Safran M, Chalifa-Caspi V, Shmueli O, Olender T, Lapidot M, Rosen N, Shmoish M, Peter Y, Glusman G, Feldmesser E, et al.: Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE. Nucleic Acids Res 2003, 31(1):142\u2013146. 10.1093\/nar\/gkg050","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"2364_CR25","doi-asserted-by":"publisher","first-page":"738","DOI":"10.1093\/bioinformatics\/btm559","volume":"24","author":"S Draghici","year":"2008","unstructured":"Draghici S, Tarca AL, Yu L, Ethier S, Romero R: KUTE-BASE: storing, downloading and exporting MIAME-compliant microarray experiments in minutes rather than hours. Bioinformatics 2008, 24(5):738\u2013740. 10.1093\/bioinformatics\/btm559","journal-title":"Bioinformatics"},{"key":"2364_CR26","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1186\/1471-2105-7-489","volume":"7","author":"TF Rayner","year":"2006","unstructured":"Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, et al.: A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics 2006, 7: 489. 10.1186\/1471-2105-7-489","journal-title":"BMC Bioinformatics"},{"issue":"9","key":"2364_CR27","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1038\/ncponc0587","volume":"3","author":"A Abdullah-Sayani","year":"2006","unstructured":"Abdullah-Sayani A, Bueno-de-Mesquita JM, Vijver MJ: Technology Insight: tuning into the genetic orchestra using microarrays\u2013limitations of DNA microarrays in clinical practice. Nat Clin Pract Oncol 2006, 3(9):501\u2013516. 10.1038\/ncponc0587","journal-title":"Nat Clin Pract Oncol"},{"issue":"9458","key":"2364_CR28","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1016\/S0140-6736(05)17866-0","volume":"365","author":"S Michiels","year":"2005","unstructured":"Michiels S, Koscielny S, Hill C: Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet 2005, 365(9458):488\u2013492. 10.1016\/S0140-6736(05)17866-0","journal-title":"Lancet"},{"issue":"5845","key":"2364_CR29","doi-asserted-by":"publisher","first-page":"1687","DOI":"10.1126\/science.1147475","volume":"317","author":"AL McGuire","year":"2007","unstructured":"McGuire AL, Cho MK, McGuire SE, Caulfield T: Medicine. The future of personal genomics. Science 2007, 317(5845):1687. 10.1126\/science.1147475","journal-title":"Science"},{"issue":"2","key":"2364_CR30","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1038\/nrg2302","volume":"9","author":"AL McGuire","year":"2008","unstructured":"McGuire AL, Caulfield T, Cho MK: Research ethics and the challenge of whole-genome sequencing. Nat Rev Genet 2008, 9(2):152\u2013156. 10.1038\/nrg2302","journal-title":"Nat Rev Genet"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-379.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T03:15:56Z","timestamp":1630466156000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-379"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,9,18]]},"references-count":30,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["2364"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-379","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,9,18]]},"assertion":[{"value":"22 May 2008","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 September 2008","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 September 2008","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"379"}}