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Comparative and Functional Genomics - Volume 4 2003, Issue 1, Pages 127-132

Conference review

Department of Genetics and Center for Bioinformatics, University of Pennsylvania, 1415 Blockley Hall, 423 Guardian Drive, Philadelphia 19104, PA , USA

European 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.


The Microarray Gene Expression Data MGED society was formed with an initial focus on experiments involving microarray technology. Despite the diversity ofapplications, there are common concepts used and a common need to captureexperimental information in a standardized manner. In building the MGED ontology,it was recognized that it would be impractical to cover all the different types ofexperiments on all the different types of organisms by listing and defining all thetypes of organisms and their properties. Our solution was to create a framework fordescribing microarray experiments with an initial focus on the biological sample andits manipulation. For concepts that are common for many species, we could provide amanageable listing of controlled terms. For concepts that are species-specific or whosevalues cannot be readily listed, we created an ‘OntologyEntry’ concept that referencedan external resource. The MGED ontology is a work in progress that needs additionalinstances and particularly needs constraints to be added. The ontology currentlycovers the experimental sample and design, and we have begun capturing aspects ofthe microarrays themselves as well. The primary application of the ontology will beto develop forms for entering information into databases, and consequently allowingqueries, taking advantage of the structure provided by the ontology. The applicationof an ontology of experimental conditions extends beyond microarray experimentsand, as the scope of MGED includes other aspects of functional genomics, so too willthe MGED ontology.

Autor: Christian J. Stoeckert Jr. and Helen Parkinson



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