{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,26]],"date-time":"2023-01-26T05:20:13Z","timestamp":1674710413490},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1644,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Meta-analysis of large gene expression datasets obtained from public repositories requires consistently annotated data. Curation of such experiments, however, is an expert activity which involves repetitive manipulation of text. Existing tools for automated curation are few, which bottleneck the analysis pipeline.<\/jats:p>\n               <jats:p>Results: We present MageComet, a web application for biologists and annotators that facilitates the re-annotation of gene expression experiments in MAGE-TAB format. It incorporates data mining, automatic annotation, use of ontologies and data validation to improve the consistency and quality of experimental meta-data from the ArrayExpress Repository.<\/jats:p>\n               <jats:p>Availability and implementation: Source and tutorials for MageComet are openly available at goo.gl\/8LQPR under the GNU GPL v3 licenses. An implementation can be found at goo.gl\/IdCuA<\/jats:p>\n               <jats:p>Contact: \u00a0parkinson@ebi.ac.uk or xue.vin@gmail.com<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts148","type":"journal-article","created":{"date-parts":[[2012,4,4]],"date-time":"2012-04-04T00:44:21Z","timestamp":1333500261000},"page":"1402-1403","source":"Crossref","is-referenced-by-count":1,"title":["MageComet\u2014web application for harmonizing existing large-scale experiment descriptions"],"prefix":"10.1093","volume":"28","author":[{"given":"Vincent","family":"Xue","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, Hunter College, City University of New York, NY 10065, USA, 2EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD and 3Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK"}]},{"given":"Tony","family":"Burdett","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Hunter College, City University of New York, NY 10065, USA, 2EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD and 3Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK"}]},{"given":"Margus","family":"Lukk","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Hunter College, City University of New York, NY 10065, USA, 2EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD and 3Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK"}]},{"given":"Julie","family":"Taylor","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Hunter College, City University of New York, NY 10065, USA, 2EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD and 3Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK"}]},{"given":"Alvis","family":"Brazma","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Hunter College, City University of New York, NY 10065, USA, 2EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD and 3Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK"}]},{"given":"Helen","family":"Parkinson","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Hunter College, City University of New York, NY 10065, USA, 2EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD and 3Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK"}]}],"member":"286","published-online":{"date-parts":[[2012,4,2]]},"reference":[{"key":"2023012512303356200_B1","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1186\/1471-2105-12-218","article-title":"OntoCAT\u2013simple ontology search and integration in Java, R and REST\/JavaScript","volume":"12","author":"Adamusiak","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023012512303356200_B2","first-page":"1958","article-title":"Cancer Genome Atlas","volume":"296","author":"Hampton","year":"2006","journal-title":"J. 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Assoc."},{"key":"2023012512303356200_B3","doi-asserted-by":"crossref","first-page":"1112","DOI":"10.1093\/bioinformatics\/btq099","article-title":"Modeling sample variables with an Experimental Factor Ontology","volume":"26","author":"Malone","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512303356200_B4","doi-asserted-by":"crossref","first-page":"D868","DOI":"10.1093\/nar\/gkn889","article-title":"ArrayExpress update\u2013from an archive of functional genomics experiments to the atlas of gene expression","volume":"37","author":"Parkinson","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012512303356200_B5","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1186\/1471-2105-7-489","article-title":"A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB","volume":"7","author":"Rayner","year":"2006","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/10\/1402\/48866041\/bioinformatics_28_10_1402.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/10\/1402\/48866041\/bioinformatics_28_10_1402.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T15:56:45Z","timestamp":1674662205000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/10\/1402\/212731"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,4,2]]},"references-count":5,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2012,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts148","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,5,15]]},"published":{"date-parts":[[2012,4,2]]}}}