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Bioinformatics Advance Access originally published online on January 21, 2006
Bioinformatics 2006 22(7):866-873; doi:10.1093/bioinformatics/btl005
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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,*

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

*To whom correspondence should be addressed.

Motivation: The generation of large amounts of microarray data and the need to share these 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 Microarray Gene Expression 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, i.e. 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).

Contact: Stoeckrt{at}pcbi.upenn.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Received on July 14, 2005; revised on January 6, 2006; accepted on January 13, 2006

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