{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:22Z","timestamp":1740185122050,"version":"3.37.3"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2019,6,22]],"date-time":"2019-06-22T00:00:00Z","timestamp":1561161600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/P50564X\/1"],"award-info":[{"award-number":["EP\/P50564X\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The human karyotype has been used as a mechanism for describing and detecting gross abnormalities in the genome for many decades. It is used both for routine diagnostic purposes and for research to further our understanding of the causes of disease. Despite these important applications there has been no rigorous computational representation of the karyotype; rather an informal, string-based representation is used, making it hard to check, organize and search data of this form. In this article, we describe our use of OWL, the Ontology Web Language, to generate a fully computational representation of the karyotype; the development of this ontology represents a significant advance from the traditional bioinformatics use for tagging and navigation and has necessitated the development of a new ontology development environment called Tawny-OWL.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The Karyotype Ontology and associated Tawny-OWL source code is available on GitHub at https:\/\/github.com\/jaydchan\/tawny-karyotype, under a LGPL License, Version 3.0.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz440","type":"journal-article","created":{"date-parts":[[2019,6,18]],"date-time":"2019-06-18T19:14:38Z","timestamp":1560885278000},"page":"5264-5270","source":"Crossref","is-referenced-by-count":0,"title":["A fully computational and reasonable representation for karyotypes"],"prefix":"10.1093","volume":"35","author":[{"given":"Jennifer D","family":"Warrender","sequence":"first","affiliation":[{"name":"School of Computing, Newcastle University , Newcastle-upon-Tyne NE4 5TG, UK"}]},{"given":"Anthony V","family":"Moorman","sequence":"additional","affiliation":[{"name":"Northern Institute for Cancer Research, Newcastle University , Newcastle-upon-Tyne NE1 7RU, UK"}]},{"given":"Phillip","family":"Lord","sequence":"additional","affiliation":[{"name":"School of Computing, Newcastle University , Newcastle-upon-Tyne NE4 5TG, UK"}]}],"member":"286","published-online":{"date-parts":[[2019,6,22]]},"reference":[{"key":"2023013108385301900_btz440-B1","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1186\/s13326-017-0159-4","article-title":"A document-centric approach for developing the tolAPC ontology","volume":"8","author":"Blfgeh","year":"2017","journal-title":"J Biomed Semantics"},{"key":"2023013108385301900_btz440-B2","first-page":"1","article-title":"Putting OWL in order: patterns for sequences in OWL","author":"Drummond","year":"2006","journal-title":"Concrete"},{"key":"2023013108385301900_btz440-B3","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1016\/j.jbi.2004.09.001","article-title":"Modeling a description logic vocabulary for cancer research","volume":"38","author":"Hartel","year":"2005","journal-title":"J. Biomed. Inform"},{"key":"2023013108385301900_btz440-B4","doi-asserted-by":"crossref","first-page":"23.","DOI":"10.1186\/s13321-015-0068-4","article-title":"InChI, the IUPAC International Chemical Identifier","volume":"7","author":"Heller","year":"2015","journal-title":"J. Cheminform"},{"key":"2023013108385301900_btz440-B5","doi-asserted-by":"crossref","first-page":"11","DOI":"10.3233\/SW-2011-0025","article-title":"The OWL API: a Java API for OWL ontologies","volume":"2","author":"Horridge","year":"2011","journal-title":"Semant. Web"},{"year":"2012","author":"Horridge","key":"2023013108385301900_btz440-B6"},{"year":"2010","author":"Jupp","key":"2023013108385301900_btz440-B7"},{"year":"2013","author":"Lord","key":"2023013108385301900_btz440-B8"},{"key":"2023013108385301900_btz440-B9","doi-asserted-by":"crossref","first-page":"7.","DOI":"10.1371\/journal.pone.0012258","article-title":"Adding a little reality to building ontologies for biology","volume":"5","author":"Lord","year":"2010","journal-title":"PLoS One"},{"volume-title":"ISCN 2013: An International System for Human Cytogenetic Nomenclature (2013)","year":"2012","author":"Shaffer","key":"2023013108385301900_btz440-B10"},{"volume-title":"Handbook on Ontologies. International Handbooks on Information Systems","year":"2009","author":"Stevens","key":"2023013108385301900_btz440-B11"},{"year":"2014","author":"Vasant","key":"2023013108385301900_btz440-B12"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz440\/29025220\/btz440.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/24\/5264\/48978618\/bioinformatics_35_24_5264.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/24\/5264\/48978618\/bioinformatics_35_24_5264.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T17:57:19Z","timestamp":1675187839000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/24\/5264\/5522010"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,6,22]]},"references-count":12,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2019,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz440","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2019,12,15]]},"published":{"date-parts":[[2019,6,22]]}}}