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{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,12,30]],"date-time":"2024-12-30T18:18:56Z","timestamp":1735582736463},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2405,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,4,15]]},"abstract":"Abstract<\/jats:title>\n Motivation: Describing biological sample variables with ontologies is complex due to the cross-domain nature of experiments. Ontologies provide annotation solutions; however, for cross-domain investigations, multiple ontologies are needed to represent the data. These are subject to rapid change, are often not interoperable and present complexities that are a barrier to biological resource users.<\/jats:p>\n Results: We present the Experimental Factor Ontology, designed to meet cross-domain, application focused use cases for gene expression data. We describe our methodology and open source tools used to create the ontology. These include tools for creating ontology mappings, ontology views, detecting ontology changes and using ontologies in interfaces to enhance querying. The application of reference ontologies to data is a key problem, and this work presents guidelines on how community ontologies can be presented in an application ontology in a data-driven way.<\/jats:p>\n Availability: \u00a0http:\/\/www.ebi.ac.uk\/efo<\/jats:p>\n Contact: \u00a0malone@ebi.ac.uk<\/jats:p>\n Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq099","type":"journal-article","created":{"date-parts":[[2010,3,4]],"date-time":"2010-03-04T01:18:36Z","timestamp":1267665516000},"page":"1112-1118","source":"Crossref","is-referenced-by-count":455,"title":["Modeling sample variables with an Experimental Factor Ontology"],"prefix":"10.1093","volume":"26","author":[{"given":"James","family":"Malone","sequence":"first","affiliation":[{"name":"1 Microarray Informatics Team, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and 2 Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA"}]},{"given":"Ele","family":"Holloway","sequence":"additional","affiliation":[{"name":"1 Microarray Informatics Team, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and 2 Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA"}]},{"given":"Tomasz","family":"Adamusiak","sequence":"additional","affiliation":[{"name":"1 Microarray Informatics Team, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and 2 Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA"}]},{"given":"Misha","family":"Kapushesky","sequence":"additional","affiliation":[{"name":"1 Microarray Informatics Team, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and 2 Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA"}]},{"given":"Jie","family":"Zheng","sequence":"additional","affiliation":[{"name":"1 Microarray Informatics Team, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and 2 Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA"}]},{"given":"Nikolay","family":"Kolesnikov","sequence":"additional","affiliation":[{"name":"1 Microarray Informatics Team, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and 2 Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA"}]},{"given":"Anna","family":"Zhukova","sequence":"additional","affiliation":[{"name":"1 Microarray Informatics Team, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and 2 Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA"}]},{"given":"Alvis","family":"Brazma","sequence":"additional","affiliation":[{"name":"1 Microarray Informatics Team, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and 2 Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA"}]},{"given":"Helen","family":"Parkinson","sequence":"additional","affiliation":[{"name":"1 Microarray Informatics Team, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and 2 Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,3,3]]},"reference":[{"key":"2023012508080944900_B1","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi0702s23","article-title":"The Gene Ontology (GO) project: structured vocabularies for molecular biology and their application to genome and expression analysis","author":"Blake","year":"2008","journal-title":"Curr. 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