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Comparative and Functional Genomics
Volume 4 (2003), Issue 1, Pages 127-132
http://dx.doi.org/10.1002/cfg.234
Conference review

The MGED Ontology: A Framework for Describing Functional Genomics Experiments

1Department of Genetics and Center for Bioinformatics, University of Pennsylvania, 1415 Blockley Hall, 423 Guardian Drive, Philadelphia 19104, PA , USA
2European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Received 14 November 2002; Accepted 19 November 2002

Copyright © 2003 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The Microarray Gene Expression Data (MGED) society was formed with an initial focus on experiments involving microarray technology. Despite the diversity of applications, there are common concepts used and a common need to capture experimental information in a standardized manner. In building the MGED ontology, it was recognized that it would be impractical to cover all the different types of experiments on all the different types of organisms by listing and defining all the types of organisms and their properties. Our solution was to create a framework for describing microarray experiments with an initial focus on the biological sample and its manipulation. For concepts that are common for many species, we could provide a manageable listing of controlled terms. For concepts that are species-specific or whose values cannot be readily listed, we created an ‘OntologyEntry’ concept that referenced an external resource. The MGED ontology is a work in progress that needs additional instances and particularly needs constraints to be added. The ontology currently covers the experimental sample and design, and we have begun capturing aspects of the microarrays themselves as well. The primary application of the ontology will be to develop forms for entering information into databases, and consequently allowing queries, taking advantage of the structure provided by the ontology. The application of an ontology of experimental conditions extends beyond microarray experiments and, as the scope of MGED includes other aspects of functional genomics, so too will the MGED ontology.