{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T16:39:03Z","timestamp":1761237543902},"reference-count":41,"publisher":"Springer Science and Business Media LLC","issue":"S6","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>A survey of microarray databases reveals that most of the repository contents and data models are heterogeneous (i.e., data obtained from different chip manufacturers), and that the repositories provide only basic biological keywords linking to PubMed. As a result, it is difficult to find datasets using research context or analysis parameters information beyond a few keywords. For example, to reduce the \"curse-of-dimension\" problem in microarray analysis, the number of samples is often increased by merging array data from different datasets. Knowing chip data parameters such as pre-processing steps (e.g., normalization, artefact removal, etc), and knowing any previous biological validation of the dataset is essential due to the heterogeneity of the data. However, most of the microarray repositories do not have meta-data information in the first place, and do not have a a mechanism to add or insert this information. Thus, there is a critical need to create \"intelligent\" microarray repositories that (1) enable update of meta-data with the raw array data, and (2) provide standardized archiving protocols to minimize bias from the raw data sources.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>To address the problems discussed, we have developed a community maintained system called ArrayWiki that unites disparate meta-data of microarray meta-experiments from multiple primary sources with four key features. First, ArrayWiki provides a user-friendly knowledge management interface in addition to a programmable interface using standards developed by Wikipedia. Second, ArrayWiki includes automated quality control processes (caCORRECT) and novel visualization methods (BioPNG, Gel Plots), which provide extra information about data quality unavailable in other microarray repositories. Third, it provides a user-curation capability through the familiar Wiki interface. Fourth, ArrayWiki provides users with simple text-based searches across all experiment meta-data, and exposes data to search engine crawlers (Semantic Agents) such as Google to further enhance data discovery.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Microarray data and meta information in ArrayWiki are distributed and visualized using a novel and compact data storage format, BioPNG. Also, they are open to the research community for curation, modification, and contribution. By making a small investment of time to learn the syntax and structure common to all sites running MediaWiki software, domain scientists and practioners can all contribute to make better use of microarray technologies in research and medical practices. ArrayWiki is available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.bio-miblab.org\/arraywiki\" ext-link-type=\"uri\">http:\/\/www.bio-miblab.org\/arraywiki<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-9-s6-s18","type":"journal-article","created":{"date-parts":[[2008,5,28]],"date-time":"2008-05-28T18:15:34Z","timestamp":1211998534000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses"],"prefix":"10.1186","volume":"9","author":[{"given":"Todd H","family":"Stokes","sequence":"first","affiliation":[]},{"given":"JT","family":"Torrance","sequence":"additional","affiliation":[]},{"given":"Henry","family":"Li","sequence":"additional","affiliation":[]},{"given":"May D","family":"Wang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2008,5,28]]},"reference":[{"key":"2629_CR1","doi-asserted-by":"publisher","first-page":"490","DOI":"10.1038\/ng1031","volume":"32","author":"GA Churchill","year":"2002","unstructured":"Churchill GA: Fundamentals of experimental design for cDNA microarrays. Nature Genetics 2002, 32: 490\u2013495.","journal-title":"Nature Genetics"},{"key":"2629_CR2","doi-asserted-by":"publisher","first-page":"S38","DOI":"10.1038\/ng1561","volume":"37","author":"E Segal","year":"2005","unstructured":"Segal E, Friedman N, Kaminski N, Regev A, Koller D: From signatures to models: understanding cancer using microarrays. Nature Genetics 2005, 37: S38-S45.","journal-title":"Nature Genetics"},{"issue":"4","key":"2629_CR3","doi-asserted-by":"publisher","first-page":"800","DOI":"10.1021\/nl0603350","volume":"6","author":"TT Zhang","year":"2006","unstructured":"Zhang TT, Stilwell JL, Gerion D, Ding LH, Elboudwarej O, Cooke PA, Gray JW, Alivisatos AP, Chen FF: Cellular effect of high doses of silica-coated quantum dot profiled with high throughput gene expression analysis and high content cellomics measurements. Nano Letters 2006,6(4):800\u2013808.","journal-title":"Nano Letters"},{"issue":"5795","key":"2629_CR4","doi-asserted-by":"publisher","first-page":"1929","DOI":"10.1126\/science.1132939","volume":"313","author":"J Lamb","year":"2006","unstructured":"Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, Wrobel MJ, Lerner J, Brunet JP, Subramanian A, Ross KN, et al.: The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science 2006,313(5795):1929\u20131935.","journal-title":"Science"},{"issue":"9","key":"2629_CR5","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1038\/nbt1239","volume":"24","author":"LM Shi","year":"2006","unstructured":"Shi LM, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, et al.: The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nature Biotechnology 2006,24(9):1151\u20131161.","journal-title":"Nature Biotechnology"},{"issue":"5","key":"2629_CR6","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1038\/nmeth756","volume":"2","author":"RA Irizarry","year":"2005","unstructured":"Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JGN, Geoghegan J, Germino G, et al.: Multiple-laboratory comparison of microarray platforms. Nature Methods 2005,2(5):345\u2013349.","journal-title":"Nature Methods"},{"issue":"9","key":"2629_CR7","doi-asserted-by":"publisher","first-page":"1123","DOI":"10.1038\/nbt1241","volume":"24","author":"R Shippy","year":"2006","unstructured":"Shippy R, Fulmer-Smentek S, Jensen RV, Jones WD, Wolber PK, Johnson CD, Pine PS, Boysen C, Guo X, Chudin E, et al.: Using RNA sample titrations to assess microarray platform performance and normalization techniques. Nature Biotechnology 2006,24(9):1123\u20131131.","journal-title":"Nature Biotechnology"},{"key":"2629_CR8","volume-title":"Bmc Bioinformatics","author":"FF Millenaar","year":"2006","unstructured":"Millenaar FF, Okyere J, May ST, van Zanten M, Voesenek LACJ, Peeters AJM: How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results. Bmc Bioinformatics 2006., 7:"},{"key":"2629_CR9","volume-title":"Bmc Bioinformatics","author":"J Seo","year":"2006","unstructured":"Seo J, Hoffman EP: Probe set algorithms: is there a rational best bet? Bmc Bioinformatics 2006., 7:"},{"key":"2629_CR10","volume-title":"Technical Note","author":"Affymetrix, Inc","year":"2005","unstructured":"Affymetrix, Inc: Guide to Probe Logarithmic Intensity Error (PLIER) Estimation. Technical Note 2005."},{"issue":"10","key":"2629_CR11","doi-asserted-by":"publisher","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","volume":"5","author":"RC Gentleman","year":"2004","unstructured":"Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al.: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004,5(10):R80.","journal-title":"Genome Biol"},{"key":"2629_CR12","doi-asserted-by":"publisher","first-page":"D562","DOI":"10.1093\/nar\/gki022","volume":"33","author":"T Barrett","year":"2005","unstructured":"Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P, Rudnev D, Lash AE, Fujibuchi W, Edgar R: NCBI GEO: mining millions of expression profiles \u2013 database and tools. Nucleic Acids Research 2005, 33: D562-D566.","journal-title":"Nucleic Acids Research"},{"key":"2629_CR13","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, Farne A, Lara GG, Holloway E, Kapushesky M, et al.: ArrayExpress \u2013 a public repository for microarray gene expression data at the EBI. Nucleic Acids Research 2005, 33: D553-D555.","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"2629_CR14","doi-asserted-by":"publisher","first-page":"133","DOI":"10.2174\/156652407779940431","volume":"7","author":"DA Hanauer","year":"2007","unstructured":"Hanauer DA, Rhodes DR, Sinha-Kumar C, Chinnaiyan AM: Bioinformatics approaches in the study of cancer. Current molecular medicine 2007,7(1):133\u2013141.","journal-title":"Current molecular medicine"},{"key":"2629_CR15","doi-asserted-by":"publisher","first-page":"D580","DOI":"10.1093\/nar\/gki006","volume":"33","author":"CA Ball","year":"2005","unstructured":"Ball CA, Awad IAB, Demeter J, Gollub J, Hebert JM, Hernandez-Boussard T, Jin H, Matese JC, Nitzberg M, Wymore F, et al.: The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Research 2005, 33: D580-D582.","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"2629_CR16","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S1476-5586(04)80047-2","volume":"6","author":"DR Rhodes","year":"2004","unstructured":"Rhodes DR, Yu JJ, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM: ONCOMINE: A cancer microarray database and integrated data-mining platform. Neoplasia 2004,6(1):1\u20136.","journal-title":"Neoplasia"},{"issue":"2","key":"2629_CR17","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1593\/neo.07112","volume":"9","author":"DR Rhodes","year":"2007","unstructured":"Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, Briggs BB, Barrette TR, Anstet MJ, Kincead-Beal C, Kulkarni P, et al.: Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia 2007,9(2):166\u2013180.","journal-title":"Neoplasia"},{"key":"2629_CR18","first-page":"D614","volume-title":"Nucleic Acids Res","author":"L Shen","year":"2005","unstructured":"Shen L, Gong J, Caldo RA, Nettleton D, Cook D, Wise RP, Dickerson JA: BarleyBase \u2013 an expression profiling database for plant genomics. Nucleic Acids Res 2005, (33 Database):D614\u2013618."},{"key":"2629_CR19","unstructured":"University of North Carolina Microarray DB"},{"issue":"6","key":"2629_CR20","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.","journal-title":"Genome Biol"},{"issue":"7","key":"2629_CR21","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 LJ, 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.","journal-title":"Bioinformatics"},{"issue":"4","key":"2629_CR22","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","volume":"19","author":"M Hucka","year":"2003","unstructured":"Hucka M, Finney A, et al.: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003,19(4):524\u2013531.","journal-title":"Bioinformatics"},{"issue":"13","key":"2629_CR23","doi-asserted-by":"publisher","first-page":"937","DOI":"10.1016\/S1359-6446(05)03501-4","volume":"10","author":"JS Luciano","year":"2005","unstructured":"Luciano JS: PAX of mind for pathway researchers. Drug Discovery Today 2005,10(13):937\u2013942.","journal-title":"Drug Discovery Today"},{"issue":"24","key":"2629_CR24","doi-asserted-by":"publisher","first-page":"4401","DOI":"10.1093\/bioinformatics\/bti718","volume":"21","author":"L Stromback","year":"2005","unstructured":"Stromback L, Lambrix P: Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX. Bioinformatics 2005,21(24):4401\u20134407.","journal-title":"Bioinformatics"},{"key":"2629_CR25","volume-title":"J Am Med Inform Assoc","author":"S Oster","year":"2007","unstructured":"Oster S, Langella S, Hastings S, Ervin D, Madduri R, Phillips J, Kurc T, Siebenlist F, Covitz P, Shanbhag K, et al.: caGrid 1.0: An Enterprise Grid Infrastructure for Biomedical Research. J Am Med Inform Assoc 2007."},{"issue":"1","key":"2629_CR26","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1186\/gb-2007-8-1-102","volume":"8","author":"SL Salzberg","year":"2007","unstructured":"Salzberg SL: Genome re-annotation: a wiki solution? Genome Biol 2007,8(1):102.","journal-title":"Genome Biol"},{"key":"2629_CR27","doi-asserted-by":"publisher","first-page":"D422","DOI":"10.1093\/nar\/gkl881","volume":"35","author":"BI Arshinoff","year":"2007","unstructured":"Arshinoff BI, Suen G, Just EM, Merchant SM, Kibbe WA, Chisholm RL, Welch RD: Xanthusbase: adapting wikipedia principles to a model organism database. Nucleic Acids Research 2007, 35: D422-D426.","journal-title":"Nucleic Acids Research"},{"issue":"7129","key":"2629_CR28","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1038\/445691a","volume":"445","author":"J Giles","year":"2007","unstructured":"Giles J: Key biology databases go wiki. Nature 2007,445(7129):691\u2013691.","journal-title":"Nature"},{"issue":"7094","key":"2629_CR29","doi-asserted-by":"publisher","first-page":"678","DOI":"10.1038\/441678a","volume":"441","author":"H Pearson","year":"2006","unstructured":"Pearson H: Online methods share insider tricks. Nature 2006,441(7094):678.","journal-title":"Nature"},{"issue":"7582","key":"2629_CR30","doi-asserted-by":"publisher","first-page":"1283","DOI":"10.1136\/bmj.39062.555405.80","volume":"333","author":"D Giustini","year":"2006","unstructured":"Giustini D: How Web 2.0 is changing medicine \u2013 Is a medical wikipedia the next step? British Medical Journal 2006,333(7582):1283\u20131284.","journal-title":"British Medical Journal"},{"key":"2629_CR31","doi-asserted-by":"publisher","first-page":"580","DOI":"10.1007\/11893011_74","volume":"4253","author":"N Fernandez-Garcia","year":"2006","unstructured":"Fernandez-Garcia N, Blazquez-del-Toro JM, Fisteus JA, Sanchez-Fernandez L: A semantic web portal for semantic annotation and search. Knowledge-Based Intelligent Information and Engineering Systems, Pt 3, Proceedings 2006, 4253: 580\u2013587.","journal-title":"Knowledge-Based Intelligent Information and Engineering Systems, Pt 3, Proceedings"},{"key":"2629_CR32","volume-title":"Wikinomics: how mass collaboration changes everything","author":"D Tapscott","year":"2006","unstructured":"Tapscott D, Williams AD: Wikinomics: how mass collaboration changes everything. New York: Portfolio; 2006."},{"key":"2629_CR33","volume-title":"Journal of Computer-Mediated Communication","author":"U Pfeil","year":"2006","unstructured":"Pfeil U, Zaphiris P, Ang CS: Cultural differences in collaborative authoring of wikipedia. Journal of Computer-Mediated Communication 2006.,12(1):"},{"issue":"2","key":"2629_CR34","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1016\/S1525-1578(10)60547-8","volume":"7","author":"AN Schuetz","year":"2005","unstructured":"Schuetz AN, Yin-Goen Q, Amin MB, Moreno CS, Cohen C, Hornsby CD, Yang WL, Petros JA, Issa MM, Pattaras JG, et al.: Molecular classification of renal tumors by gene expression profiling. J Mol Diagn 2005,7(2):206\u2013218.","journal-title":"J Mol Diagn"},{"issue":"1","key":"2629_CR35","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1097\/PAP.0b013e3181594720","volume":"15","author":"AN Young","year":"2008","unstructured":"Young AN, Master VA, Paner GP, Wang MD, Amin MB: Renal Epithelial Neoplasms: Diagnostic Applications of Gene Expression Profiling. Adv Anat Pathol 2008,15(1):28\u201338.","journal-title":"Adv Anat Pathol"},{"issue":"6","key":"2629_CR36","doi-asserted-by":"publisher","first-page":"1068","DOI":"10.1007\/s10439-007-9313-y","volume":"35","author":"TH Stokes","year":"2007","unstructured":"Stokes TH, Moffitt RA, Phan JH, Wang MD: chip artifact CORRECTion (caCORRECT): A Bioinformatics System for Quality Assurance of Genomics and Proteomics Array Data. Ann Biomed Eng 2007,35(6):1068\u20131080.","journal-title":"Ann Biomed Eng"},{"issue":"23\u201324","key":"2629_CR37","doi-asserted-by":"publisher","first-page":"1689","DOI":"10.1016\/S1359-6446(05)03647-0","volume":"10","author":"Y Luo","year":"2005","unstructured":"Luo Y, Lonardi S: Storage and transmission of microarray images. Drug Discovery Today 2005,10(23\u201324):1689\u20131695.","journal-title":"Drug Discovery Today"},{"key":"2629_CR38","first-page":"196","volume-title":"Life Science Systems and Applications Workshop, 2007 LISA 2007 IEEE\/NIH. Bethesda, MD","author":"JT Torrance","year":"2007","unstructured":"Torrance JT, Moffitt RA, Stokes TH, Wang MD: Can we trust biomarkers? visualization and quantification of outlier probes in high density oligonucleotide microarrays. Life Science Systems and Applications Workshop, 2007 LISA 2007 IEEE\/NIH. Bethesda, MD 2007, 196\u2013199."},{"issue":"1 Suppl","key":"2629_CR39","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1038\/4434","volume":"21","author":"DJ Duggan","year":"1999","unstructured":"Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM: Expression profiling using cDNA microarrays. Nat Genet 1999,21(1 Suppl):10\u201314.","journal-title":"Nat Genet"},{"key":"2629_CR40","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1093\/bioinformatics\/btm229","volume":"23","author":"WA Baumgartner","year":"2007","unstructured":"Baumgartner WA, Cohen KB, Fox LM, Acquaah-Mensah G, Hunter L: Manual curation is not sufficient for annotation of genomic databases. Bioinformatics 2007, 23: 141\u2013148.","journal-title":"Bioinformatics"},{"key":"2629_CR41","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1109\/MIC.2007.110","volume":"11","author":"M Hepp","year":"2007","unstructured":"Hepp M, Siorpaes K, Bachlechner D: Harvesting Wiki consensus - Using wikipedia entries as vocabulary for knowledge management. Ieee Internet Computing 2007, 11: 54\u201365.","journal-title":"Ieee Internet Computing"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-S6-S18.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T08:23:47Z","timestamp":1630484627000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-S6-S18"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,5,28]]},"references-count":41,"journal-issue":{"issue":"S6","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["2629"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-s6-s18","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,5,28]]},"assertion":[{"value":"28 May 2008","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S18"}}