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

@article{citeulike:2821781, abstract = {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@pcbi.upenn.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, address = {Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, USA.}, author = {Whetzel, P. L. and Parkinson, H. and Causton, H. C. and Fan, L. and Fostel, J. and Fragoso, G. and Game, L. and Heiskanen, M. and Morrison, N. and Rocca-Serra, P. and Sansone, S. A. and Taylor, C. and White, J. and Stoeckert, C. J. }, citeulike-article-id = {2821781}, issn = {1367-4803}, journal = {Bioinformatics (Oxford, England)}, keywords = {microarray}, month = {April}, number = {7}, pages = {866--873}, posted-at = {2008-05-22 03:14:17}, priority = {2}, title = {The MGED Ontology: a resource for semantics-based description of microarray experiments.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/16428806}, volume = {22}, year = {2006} }

TY - JOUR ID - citeulike:2821781 L3 - citeulike-article-id:2821781 TI - The MGED Ontology: a resource for semantics-based description of microarray experiments. JF - Bioinformatics (Oxford, England) VL - 22 IS - 7 SP - 866 EP - 873 AD - Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, USA. SN - 1367-4803 N2 - 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@pcbi.upenn.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. KW - microarray AU - Whetzel, PL AU - Parkinson, H AU - Causton, HC AU - Fan, L AU - Fostel, J AU - Fragoso, G AU - Game, L AU - Heiskanen, M AU - Morrison, N AU - Rocca-Serra, P AU - Sansone, SA AU - Taylor, C AU - White, J AU - Stoeckert, CJ PY - 2006/04/01/ UR - http://view.ncbi.nlm.nih.gov/pubmed/16428806 ER -