References
- Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001; 29(4):365-371.
- MGED (Microarray Gene Expression Data) Society [Internet]. [cited 2011 May 3] ( http://www.mged.org/
- Field D, Sansone SA. A special issue on data standards. OMICS. 2006; 10(2): 84-93.
- Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Edgar R. NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res. 2009. 37(Suppl. 1): D885-D890.
- Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A. ArrayExpress update-from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res. 2009; 37(Suppl. 1): D868-D872.
- Sugawara H, Ogasawara O, Okubo K, Gojobori T, Tateno Y. DDBJ with new system and face. Nucleic Acids Res. 2008; 36(Suppl. 1): D22-D24.
- Bioconductor, open source software for bioinformatics [Internet]. [cited 2011 May 3] ( http://www.bioconductor.org
- Zhu Y, Davis S, Stephens R, Meltzer PS, Chen Y. GEO-metadb: powerful alternative search engine for the GEO. Bioinformatics. 2008; 24(23): 2798-2800.
- Bekel T, Henckel K, Küster H, Meyer F, Mittard RV, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Pühler A, Stoye J, Goesmann A. The Sequence Analysis and Management System - SAMS 2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies. J Biotechnol. 2009; 140(1-2): 3-12.
- Te Pas MF, Hulsegge I, Coster A, Pool MH, Heuven HH, Janss LL. Biochemical pathways analysis of microarray results: regulation of myogenesis in pigs. BMC Dev Biol. 2007; 7: 66.
- Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ Jr, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A. A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics. 2006; 7: 489.
- ArrayExpress, Functional Genomics Database at European Bioinformatics Institute. [cited 2011 May 3] ( http://www.ebi.ac.uk/microarray-as/ae/
- DC (Dublin Core) Metadata Initiative [Internet]. [cited 2011 May 3] ( http://dublincore.org/
- Lors RK, van Ginneken AM, van der Lei J. OpenSDE: a strategy for expressive and flexible structured data entry. Int J Med Inform. 2005; 74(6): 481-490.
- MAQC Consortium, Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, Zhang L, Amur S, Bao W, Barbacioru CC, Lucas AB, Bertholet V, Boysen C, Bromley B, Brown D, Brunner A, Canales R, Cao XM, Cebula TA, Chen JJ, Cheng J, Chu TM, Chudin E, Corson J, Corton JC, Croner LJ, Davies C, Davison TS, Delenstarr G, Deng X, Dorris D, Eklund AC, Fan XH, Fang H, Fulmer-Smentek S, Fuscoe JC, Gallagher K, Ge W, Guo L, Guo X, Hager J, Haje PK, Han J, Han T, Harbottle HC, Harris SC, Hatchwell E, Hauser CA, Hester S, Hong H, Hurban P, Jackson SA, Ji H, Knight CR, Kuo WP, LeClerc JE, Levy S, Li QZ, Liu C, Liu Y, Lombardi MJ, Ma Y, Magnuson SR, Maqsodi B, McDaniel T, Mei N, Myklebost O, Ning B, Novoradovskaya N, Orr MS, Osborn TW, Papallo A, Patterson TA, Perkins RG, Peters EH, Peterson R, Philips KL, Pine PS, Pusztai L, Qian F, Ren H, Rosen M, Rosenzweig BA, Samaha RR, Schena M, Schroth GP, Shchegrova S, Smith DD, Staedtler F, Su Z, Sun H, Szallasi Z, Tezak Z, Thierry-Mieg D, Thompson KL, Tikhonova I, Turpaz Y, Vallanat B, Van C, Walker SJ, Wang SJ, Wang Y, Wolfinger R, Wong A, Wu J, Xiao C, Xie Q, Xu J, Yang W, Zhang L, Zhong S, Zong Y, Slikker W Jr. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol. 2006; 24(9): 1151-1161.
- Barrett T, Troup DB, S, 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 — database and tools update (MINiML). Nucleic Acids Res. 2007; 35(Suppl. 1): D760-D765.
- ISO 11179, Metadata Registries (MDR). [cited 2011 May 3] ( http://www.iso.org
- SPARQL, Query Language for RDF. [cited 2011 May 3] ( http://www.w3.org/TR/rdf-sparql-query/
- Miller H, Norton CN, Sarkar IN. Genbank and PubMed: How connected are they? BMC Res Notes. 2009; 2: 101.
- Garde S, Chen R, Leslie H, Beale T, McNicoll I, Heard S. Archetype-based knowledge management for semantic interoperability of electronic health records. Stud Health Technol Inform. 2009; 150: 1007-1011.
- REACTOME, a curated knowledgebase of biological pathways. [cited 2011 May 3] ( http://www.reactome.org
- XPath (XML Path Expression Language). [cited 2011 May 3] ( http://www.w3.org/TR/XPath
- FOAF (Friend of a Friend) Project. [cited 2011 May 3] ( http://www.foaf-project.org/
- RuleML (Rule Markup Language) Initiative. [cited 2011 May 3] ( http://www.ruleml.org/
- hcard, Format for representing people, organizations, and places. [cited 2011 May 3] ( http://www.w3.org/2006/03/hcard
- vcard (Format for electronic business cards). [cited 2011 May 3] ( http://www.w3.org/TR/vcard-rdf
- W3C PIM (Personal Information Management) Vocabulary. [cited 2011 May 3] ( http://www.w3.org/2000/10/swap/pim/
- Esposito M. An ontological and non-monotonic rulebased approach to label medical images. Third Proceedings of the Third International Institute of Electrical and Electronics Engineers (IEEE) Conference on Signal-Image Technologies and Internet-Based System (SITIS), Shanghai, People's Republic of China, 16-18 December 2007: 603-611.
- Protégé, open source ontology editor and knowledge-base framework. [cited 2011 May 3] ( http://protege.stanford.edu/
- W3C XML Schema Validator. [cited 2011 May 3] ( http://www.w3c.org/2001/03/webdata/xsv
- W3C RDF Validation Service. [cited 2011 May 3] ( http://www.w3.org/RDF/Validator/
- jDREW, A Java Deductive Reasoning Engine for the Web (SPARQL, RuleML support). [cited 2011 May 3] ( http://www.jdrew.org/
- SWRL (Semantic Web Rule Language). [cited 2011 May 3] ( http://www.w3.org/Submission/SWRL/
- W3C Rule Interchange Format. [cited 2011 May 3] ( http://www.w3.org/2005/rules/
- SPARQLer, an online RDF Query platform on the public domain. [cited 2011 May 3] ( http://www.sparql.org/query.html