{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T21:40:16Z","timestamp":1675201216598},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2685,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: For many years, the Unified Medical Language System (UMLS) semantic network (SN) has been used as an upper-level semantic framework for the categorization of terms from terminological resources in biomedicine. BioTop has recently been developed as an upper-level ontology for the biomedical domain. In contrast to the SN, it is founded upon strict ontological principles, using OWL DL as a formal representation language, which has become standard in the semantic Web. In order to make logic-based reasoning available for the resources annotated or categorized with the SN, a mapping ontology was developed aligning the SN with BioTop.<\/jats:p>\n               <jats:p>Methods: The theoretical foundations and the practical realization of the alignment are being described, with a focus on the design decisions taken, the problems encountered and the adaptations of BioTop that became necessary. For evaluation purposes, UMLS concept pairs obtained from MEDLINE abstracts by a named entity recognition system were tested for possible semantic relationships. Furthermore, all semantic-type combinations that occur in the UMLS Metathesaurus were checked for satisfiability.<\/jats:p>\n               <jats:p>Results: The effort-intensive alignment process required major design changes and enhancements of BioTop and brought up several design errors that could be fixed. A comparison between a human curator and the ontology yielded only a low agreement. Ontology reasoning was also used to successfully identify 133 inconsistent semantic-type combinations.<\/jats:p>\n               <jats:p>Availability: BioTop, the OWL DL representation of the UMLS SN, and the mapping ontology are available at http:\/\/www.purl.org\/biotop\/.<\/jats:p>\n               <jats:p>Contact: \u00a0stschulz@uni-freiburg.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp194","type":"journal-article","created":{"date-parts":[[2009,5,28]],"date-time":"2009-05-28T15:48:54Z","timestamp":1243525734000},"page":"i69-i76","source":"Crossref","is-referenced-by-count":14,"title":["Alignment of the UMLS semantic network with BioTop: methodology and assessment"],"prefix":"10.1093","volume":"25","author":[{"given":"Stefan","family":"Schulz","sequence":"first","affiliation":[{"name":"1 Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Stefan-Meier-Str. 26, 79104 Freiburg, 2Jena University Language and Information Engineering (JULIE) Lab, Germany, 3Erasmus MC, Rotterdam, The Netherlands and 4National Library of Medicine, Bethesda, MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elena","family":"Beisswanger","sequence":"additional","affiliation":[{"name":"1 Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Stefan-Meier-Str. 26, 79104 Freiburg, 2Jena University Language and Information Engineering (JULIE) Lab, Germany, 3Erasmus MC, Rotterdam, The Netherlands and 4National Library of Medicine, Bethesda, MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"L\u00e1szl\u00f3","family":"van den Hoek","sequence":"additional","affiliation":[{"name":"1 Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Stefan-Meier-Str. 26, 79104 Freiburg, 2Jena University Language and Information Engineering (JULIE) Lab, Germany, 3Erasmus MC, Rotterdam, The Netherlands and 4National Library of Medicine, Bethesda, MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olivier","family":"Bodenreider","sequence":"additional","affiliation":[{"name":"1 Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Stefan-Meier-Str. 26, 79104 Freiburg, 2Jena University Language and Information Engineering (JULIE) Lab, Germany, 3Erasmus MC, Rotterdam, The Netherlands and 4National Library of Medicine, Bethesda, MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erik M.","family":"van Mulligen","sequence":"additional","affiliation":[{"name":"1 Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Stefan-Meier-Str. 26, 79104 Freiburg, 2Jena University Language and Information Engineering (JULIE) Lab, Germany, 3Erasmus MC, Rotterdam, The Netherlands and 4National Library of Medicine, Bethesda, MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,5,27]]},"reference":[{"key":"2023013111583164300_B1","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. 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