{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T14:15:25Z","timestamp":1790086525370,"version":"4.0.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"9","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Biomedical ontologies are often very large and complex. Only a subset of the ontology may be needed for a specified application or community. For ontology end users, it is desirable to have community-based labels rather than the labels generated by ontology developers. Ontodog is a web-based system that can generate an ontology subset based on Excel input, and support generation of an ontology community view, which is defined as the whole or a subset of the source ontology with user-specified annotations including user-preferred labels. Ontodog allows users to easily generate community views with minimal ontology knowledge and no programming skills or installation required. Currently &amp;gt;100 ontologies including all OBO Foundry ontologies are available to generate the views based on user needs. We demonstrate the application of Ontodog for the generation of community views using the Ontology for Biomedical Investigations as the source ontology.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/ontodog.hegroup.org\/<\/jats:p>\n               <jats:p>Contact: \u00a0yongqunh@umich.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu008","type":"journal-article","created":{"date-parts":[[2014,1,11]],"date-time":"2014-01-11T02:06:09Z","timestamp":1389405969000},"page":"1340-1342","source":"Crossref","is-referenced-by-count":13,"title":["Ontodog: a web-based ontology community view generation tool"],"prefix":"10.1093","volume":"30","author":[{"given":"Jie","family":"Zheng","sequence":"first","affiliation":[{"name":"1 Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 and 2Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zuoshuang","family":"Xiang","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 and 2Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"Jr","given":"Christian J.","family":"Stoeckert","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 and 2Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongqun","family":"He","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 and 2Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,1,9]]},"reference":[{"key":"2023012710524227600_btu008-B1","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"2023012710524227600_btu008-B2","doi-asserted-by":"crossref","DOI":"10.1186\/2041-1480-1-S1-S7","article-title":"Modeling biomedical experimental processes with OBI","volume":"1","author":"Brinkman","year":"2010","journal-title":"J. Biomed. Semantics."},{"key":"2023012710524227600_btu008-B3","article-title":"Value sets via ontology views","volume-title":"Proceedings, Clinical Research Informatics Summit of the American Medical Informatics Association","author":"Detwiler","year":"2011"},{"key":"2023012710524227600_btu008-B4","first-page":"246","article-title":"Enriching the Ontology for Biomedical Investigations (OBI) to improve its Suitability for Web Service Annotations","volume-title":"International Conference on Biomedical Ontology (ICBO)","author":"Guttula","year":"2011"},{"key":"2023012710524227600_btu008-B6","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1186\/1756-0500-3-175","article-title":"OntoFox: web-based support for ontology reuse","volume":"3","author":"Xiang","year":"2010","journal-title":"BMC Res. Notes"},{"key":"2023012710524227600_btu008-B7","article-title":"Development of an application ontology for beta cell genomics based on the ontology for biomedical investigations","volume-title":"International Conference on Biomedical Ontologies (ICBO 2013)","author":"Zheng","year":"2013"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/9\/1340\/48922123\/bioinformatics_30_9_1340.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/9\/1340\/48922123\/bioinformatics_30_9_1340.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T11:32:43Z","timestamp":1674819163000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/9\/1340\/235578"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,1,9]]},"references-count":6,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2014,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu008","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,5,1]]},"published":{"date-parts":[[2014,1,9]]}}}