The MGED Ontology: a resource for semantics-based description of microarray experiments.
BACKGROUND
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.


BACKGROUND
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).


BACKGROUND
Stoeckrt@pcbi.upenn.edu


BACKGROUND
Supplementary data are available at Bioinformatics online.
Whetzel
Patricia L
PL
Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, USA.
Parkinson
Helen
H
Causton
Helen C
HC
Fan
Liju
L
Fostel
Jennifer
J
Fragoso
Gilberto
G
Game
Laurence
L
Heiskanen
Mervi
M
Morrison
Norman
N
Rocca-Serra
Philippe
P
Sansone
Susanna-Assunta
SA
Taylor
Chris
C
White
Joseph
J
Stoeckert
Christian J
CJ
D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D003628:Database Management Systems; D020869:Gene Expression Profiling / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011381:Programming Languages; D014584:User-Computer Interface