{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T12:33:56Z","timestamp":1775306036135,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability: The MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at . Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System ().<\/jats:p>\n               <jats:p>Contact: \u00a0Stoeckrt@pcbi.upenn.edu<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl005","type":"journal-article","created":{"date-parts":[[2006,1,22]],"date-time":"2006-01-22T01:23:04Z","timestamp":1137892984000},"page":"866-873","source":"Crossref","is-referenced-by-count":142,"title":["The MGED Ontology: a resource for semantics-based description of microarray experiments"],"prefix":"10.1093","volume":"22","author":[{"given":"Patricia L.","family":"Whetzel","sequence":"first","affiliation":[{"name":"Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine 1 \u00a0 1 \u00a0 \u00a0 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Helen","family":"Parkinson","sequence":"additional","affiliation":[{"name":"European Bioinformatics Institute 2 \u00a0 2 \u00a0 \u00a0 Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Helen C.","family":"Causton","sequence":"additional","affiliation":[{"name":"MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College 3 \u00a0 3 \u00a0 \u00a0 Hammersmith Hospital Campus, DuCane Road, London W12 0NN, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liju","family":"Fan","sequence":"additional","affiliation":[{"name":"Ontology Workshop LLC 4 \u00a0 4 \u00a0 \u00a0 PO Box 182, Columbia, MD 21045-9998, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jennifer","family":"Fostel","sequence":"additional","affiliation":[{"name":"NIEHS 5 \u00a0 5 \u00a0 \u00a0 PO Box 12233 MD F1-05, 111 Alexander Drive Research Triangle Park, NC 27709-2233, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gilberto","family":"Fragoso","sequence":"additional","affiliation":[{"name":"NCICB, NCI Center for Bioinformatics 6 \u00a0 6 \u00a0 \u00a0 6116 Executive Boulevard, Rockville, MD 20852, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laurence","family":"Game","sequence":"additional","affiliation":[{"name":"MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College 3 \u00a0 3 \u00a0 \u00a0 Hammersmith Hospital Campus, DuCane Road, London W12 0NN, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mervi","family":"Heiskanen","sequence":"additional","affiliation":[{"name":"NCICB, NCI Center for Bioinformatics 6 \u00a0 6 \u00a0 \u00a0 6116 Executive Boulevard, Rockville, MD 20852, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Norman","family":"Morrison","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Kilburn Building University of Manchester 7 \u00a0 7 \u00a0 \u00a0 Oxford Road, Manchester M13 9PL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philippe","family":"Rocca-Serra","sequence":"additional","affiliation":[{"name":"European Bioinformatics Institute 2 \u00a0 2 \u00a0 \u00a0 Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Susanna-Assunta","family":"Sansone","sequence":"additional","affiliation":[{"name":"European Bioinformatics Institute 2 \u00a0 2 \u00a0 \u00a0 Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chris","family":"Taylor","sequence":"additional","affiliation":[{"name":"European Bioinformatics Institute 2 \u00a0 2 \u00a0 \u00a0 Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joseph","family":"White","sequence":"additional","affiliation":[{"name":"Dana-Farber Cancer Institute 8 \u00a0 8 \u00a0 \u00a0 44 Binney Street, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"suffix":"Jr","given":"Christian J.","family":"Stoeckert","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine 1 \u00a0 1 \u00a0 \u00a0 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,1,21]]},"reference":[{"key":"2023012409104819500_b1","doi-asserted-by":"crossref","first-page":"D580","DOI":"10.1093\/nar\/gki006","article-title":"The Stanford Microarray Database accommodates additional microarray platforms and data formats","volume":"33","author":"Ball","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012409104819500_b2","doi-asserted-by":"crossref","first-page":"D562","DOI":"10.1093\/nar\/gki022","article-title":"NCBI GEO: mining millions of expression profiles\u2014database and tools","volume":"33","author":"Barrett","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012409104819500_b3","first-page":"396","article-title":"OilEd: a Reason-able Ontology Editor for the Semantic Web","volume":"2174","author":"Bechhofer","year":"2001","journal-title":"Proc. KI2001"},{"key":"2023012409104819500_b4","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023012409104819500_b5","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1038\/ng1201-365","article-title":"Minimum information about a microarray experiment (MIAME)-toward standards for microarray data","volume":"29","author":"Brazma","year":"2001","journal-title":"Nat. Genet."},{"key":"2023012409104819500_b6","doi-asserted-by":"crossref","first-page":"2404","DOI":"10.1093\/bioinformatics\/btg335","article-title":"caCORE: a common infrastructure for cancer informatics","volume":"19","author":"Covitz","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012409104819500_b7","doi-asserted-by":"crossref","first-page":"642","DOI":"10.1002\/cfg.446","article-title":"The Sequence Ontology","volume":"5","author":"Eilbeck","year":"2005","journal-title":"Comp. Funct. Genomics"},{"key":"2023012409104819500_b8","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1093\/bib\/2.2.143","article-title":"A comparison of microarray databases [Erratum (2001) Brief. Bioinform., 2, 220.]","volume":"2","author":"Gardiner-Garden","year":"2001","journal-title":"Brief. Bioinform."},{"key":"2023012409104819500_b9","doi-asserted-by":"crossref","first-page":"1425","DOI":"10.1101\/gr.180801","article-title":"Creating the gene ontology resource: design and implementation","volume":"11","author":"Gene Ontology Consortium.","year":"2001","journal-title":"Genome Res."},{"key":"2023012409104819500_b10","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1016\/j.crvi.2003.09.034","article-title":"CIBEX: center for information biology gene expression database","volume":"326","author":"Ikeo","year":"2003","journal-title":"C. R. Biol."},{"key":"2023012409104819500_b11","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1016\/S0006-291X(03)01215-4","article-title":"Changes in gene expression induced by H(2)O(2) in cardiac myocytes","volume":"307","author":"Kemp","year":"2003","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"2023012409104819500_b12","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1038\/nbt0705-833","article-title":"Summary recommendations for standardization and reporting of metabolic analyses","volume":"23","author":"Lindon","year":"2005","journal-title":"Nat. Biotechnol."},{"key":"2023012409104819500_b13","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1093\/bioinformatics\/btg428","article-title":"RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies","volume":"20","author":"Manduchi","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012409104819500_b14","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1289\/ehp.6697","article-title":"Database development in toxicogenomics: issues and efforts","volume":"112","author":"Mattes","year":"2004","journal-title":"Environ Health Perspect."},{"key":"2023012409104819500_b15","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1186\/1471-2105-6-268","article-title":"MiMiR: a comprehensive solution for storage, annotation and exchange of microarray data","volume":"6","author":"Navarange","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023012409104819500_b16","doi-asserted-by":"crossref","first-page":"D553","DOI":"10.1093\/nar\/gki056","article-title":"ArrayExpress\u2014a public repository for microarray gene expression data at the EBI","volume":"33","author":"Parkinson","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012409104819500_b17","first-page":"256","article-title":"GALEN ten years on: tasks and supporting tools","volume":"10","author":"Rogers","year":"2001","journal-title":"Medinfo."},{"key":"2023012409104819500_b18","doi-asserted-by":"crossref","first-page":"RESEARCH0046","DOI":"10.1186\/gb-2002-3-9-research0046","article-title":"Design and implementation of microarray gene expression markup language (MAGE-ML)","volume":"3","author":"Spellman","year":"2002","journal-title":"Genome Biol."},{"key":"2023012409104819500_b19","first-page":"53","article-title":"ChemIDplus-super source for chemical and drug information","volume":"21","author":"Tomasulo","year":"2002","journal-title":"Med. RefServ. Q"},{"key":"2023012409104819500_b20","doi-asserted-by":"crossref","first-page":"D39","DOI":"10.1093\/nar\/gki062","article-title":"Database resources of the National Center for Biotechnology Information","volume":"33","author":"Wheeler","year":"2005","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/7\/866\/48839455\/bioinformatics_22_7_866.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/7\/866\/48839455\/bioinformatics_22_7_866.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T09:44:25Z","timestamp":1674553465000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/7\/866\/202362"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,1,21]]},"references-count":20,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2006,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl005","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,4,1]]},"published":{"date-parts":[[2006,1,21]]}}}