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Bioinformatics Advance Access published online on January 21, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl005
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received July 14, 2005
Revised January 6, 2006
Accepted January 13, 2006

Article

The MGED Ontology; a resource for semantics-based description of microarray experiments

Patricia L. Whetzel 1 *, Helen Parkinson 2, Helen C. Causton 3, Liju Fan 4, Jennifer Fostel 5, Gilberto Fragoso 6, Laurence Game 3, Mervi Heiskanen 6, Norman Morrison 7, Philippe Rocca-Serra 2, Susanna-Assunta Sansone 2, Chris Taylor 2, Joseph White 8, and Christian J. Stoeckert Jr. 1

1 Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, USA
2 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
3 MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, Hammersmith Hospital Campus, DuCane Road, London W12 0NN, UK
4 Ontology Workshop LLC, P.O. Box 182, Columbia, MD 21045-9998, USA
5 NIEHS PO Box 12233 MD F1-05, 111 Alexander Drive Research Triangle Park, NC, 27709-2233, USA
6 NCICB, NCI Center for Bioinformatics, 6116 Executive Blvd, Rockville, MD 20852, USA
7 Department of Computer Science, Kilburn Building University of Manchester, Oxford Road, Manchester, M13 9PL, UK
8 Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA


  Abstract

Motivation: The generation of large amounts of microarray data and the need to share this data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the MAGE Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards.

Results: Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines that is, to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation.

Availability: The MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at: http://mged.sourceforge.net/ontologies/index.php. Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System (http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do).

Associate Editor: Alvis Brazma
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