METADATA MANAGEMENT AND SEMANTICS
IN MICROARRAY REPOSITORIES
Kocabaş F1,2,*, Can T3, Baykal N1
*Corresponding Author: Fahri Kocabaş, NATO HQ C3S, Blvd Leopold III B, 1110 Brussels, Belgium;
Tel.: +32-2-707-5533; Fax: +32-2-707-5834; E-mail: FK:fahri@ii.metu.edu.tr; f.kocabas@hq.nato.int
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REFERENCES
1. 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.
2. MGED (Microarray Gene Expression Data) Society
[Internet]. [cited 2011 May 3] (http://www.mged.org/).
3. Field D, Sansone SA. A special issue on data standards.
OMICS. 2006; 10(2): 84-93.
4. 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.
5. 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.
6. 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.
7. Bioconductor, open source software for bioinformatics
[Internet]. [cited 2011 May 3] (http://www. bioconductor.
org).
8. Zhu Y, Davis S, Stephens R, Meltzer PS, Chen Y. GEOmetadb:
powerful alternative search engine for the
GEO. Bioinformatics. 2008; 24(23): 2798-2800.
9. 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.
10. 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.
11. 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.
12. ArrayExpress, Functional Genomics Database at European
Bioinformatics Institute. [cited 2011 May 3]
(http://www.ebi.ac.uk/microarray-as/ae/).
13. DC (Dublin Core) Metadata Initiative [Internet]. [cited
2011 May 3] (http://dublincore.org/).
14. 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.
15. 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.
16. 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.
17. ISO 11179, Metadata Registries (MDR). [cited 2011
May 3] (http://www.iso.org).
18. SPARQL, Query Language for RDF. [cited 2011 May 3]
(http://www.w3.org/TR/rdf-sparql-query/).
19. Miller H, Norton CN, Sarkar IN. Genbank and PubMed:
How connected are they? BMC Res Notes. 2009; 2:
101.
20. 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.
21. REACTOME, a curated knowledgebase of biological
pathways. [cited 2011 May 3] (http://www.reactome.
org).
22. XPath (XML Path Expression Language). [cited 2011
May 3] (http://www.w3.org/TR/XPath).
23. FOAF (Friend of a Friend) Project. [cited 2011 May 3]
(http://www.foaf-project.org/).
24. RuleML (Rule Markup Language) Initiative. [cited
2011 May 3] (http://www.ruleml.org/).
25. hcard, Format for representing people, organizations,
and places. [cited 2011 May 3] (http://www.w3.org/
2006/03/hcard).
26. vcard (Format for electronic business cards). [cited
2011 May 3] (http://www.w3.org/TR/vcard-rdf).
27. W3C PIM (Personal Information Management) Vocabulary.
[cited 2011 May 3] (http://www.w3.org/2000/ 10/
swap/pim/).
28. 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.
29. Protégé, open source ontology editor and knowledgebase
framework. [cited 2011 May 3] (http:// protege.
stanford.edu/).
30. W3C XML Schema Validator. [cited 2011 May 3]
(http://www.w3c.org/2001/03/webdata/xsv).
31. W3C RDF Validation Service. [cited 2011 May 3]
(http://www.w3.org/RDF/Validator/).
32. jDREW, A Java Deductive Reasoning Engine for the
Web (SPARQL, RuleML support). [cited 2011 May 3]
(http://www.jdrew.org/).
33. SWRL (Semantic Web Rule Language). [cited 2011
May 3] (http://www.w3.org/ Submission/SWRL/).
34. W3C Rule Interchange Format. [cited 2011 May 3]
(http://www.w3.org/2005/rules/).
35. SPARQLer, an online RDF Query platform on the public
domain. [cited 2011 May 3] (http://www.sparql. org/
query.html).
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