{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,12]],"date-time":"2025-09-12T18:19:50Z","timestamp":1757701190128},"reference-count":22,"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":2315,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Recent years have seen the development of a wide range of biomedical ontologies. Notable among these is Sequence Ontology (SO) which offers a rich hierarchy of terms and relationships that can be used to annotate genomic data. Well-designed formal ontologies allow data to be reasoned upon in a consistent and logically sound way and can lead to the discovery of new relationships. The Semantic Web Rules Language (SWRL) augments the capabilities of a reasoner by allowing the creation of conditional rules. To date, however, formal reasoning, especially the use of SWRL rules, has not been widely used in biomedicine.<\/jats:p>\n               <jats:p>Results: We have built a knowledge base of human pseudogenes, extending the existing SO framework to incorporate additional attributes. In particular, we have defined the relationships between pseudogenes and segmental duplications. We then created a series of logical rules using SWRL to answer research questions and to annotate our pseudogenes appropriately. Finally, we were left with a knowledge base which could be queried to discover information about human pseudogene evolution.<\/jats:p>\n               <jats:p>Availability: The fully populated knowledge base described in this document is available for download from http:\/\/ontology.pseudogene.org. A SPARQL endpoint from which to query the dataset is also available at this location.<\/jats:p>\n               <jats:p>Contact: \u00a0matthew.holford@yale.edu; mark.gerstein@yale.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq173","type":"journal-article","created":{"date-parts":[[2010,6,7]],"date-time":"2010-06-07T07:28:13Z","timestamp":1275895693000},"page":"i71-i78","source":"Crossref","is-referenced-by-count":16,"title":["Using semantic web rules to reason on an ontology of pseudogenes"],"prefix":"10.1093","volume":"26","author":[{"given":"Matthew E.","family":"Holford","sequence":"first","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2 Department of Molecular Biophysics and Biochemistry, 3 Department of Computer Science, 4 Center for Medical Informatics and 5 Department of Genetics, Yale University, New Haven, CT 06520, USA"}]},{"given":"Ekta","family":"Khurana","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2 Department of Molecular Biophysics and Biochemistry, 3 Department of Computer Science, 4 Center for Medical Informatics and 5 Department of Genetics, Yale University, New Haven, CT 06520, USA"}]},{"given":"Kei-Hoi","family":"Cheung","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2 Department of Molecular Biophysics and Biochemistry, 3 Department of Computer Science, 4 Center for Medical Informatics and 5 Department of Genetics, Yale University, New Haven, CT 06520, USA"},{"name":"1 Program in Computational Biology and Bioinformatics, 2 Department of Molecular Biophysics and Biochemistry, 3 Department of Computer Science, 4 Center for Medical Informatics and 5 Department of Genetics, Yale University, New Haven, CT 06520, USA"},{"name":"1 Program in Computational Biology and Bioinformatics, 2 Department of Molecular Biophysics and Biochemistry, 3 Department of Computer Science, 4 Center for Medical Informatics and 5 Department of Genetics, Yale University, New Haven, CT 06520, USA"},{"name":"1 Program in Computational Biology and Bioinformatics, 2 Department of Molecular Biophysics and Biochemistry, 3 Department of Computer Science, 4 Center for Medical Informatics and 5 Department of Genetics, Yale University, New Haven, CT 06520, USA"}]},{"given":"Mark","family":"Gerstein","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2 Department of Molecular Biophysics and Biochemistry, 3 Department of Computer Science, 4 Center for Medical Informatics and 5 Department of Genetics, Yale University, New Haven, CT 06520, USA"},{"name":"1 Program in Computational Biology and Bioinformatics, 2 Department of Molecular Biophysics and Biochemistry, 3 Department of Computer Science, 4 Center for Medical Informatics and 5 Department of Genetics, Yale University, New Haven, CT 06520, USA"},{"name":"1 Program in Computational Biology and Bioinformatics, 2 Department of Molecular Biophysics and Biochemistry, 3 Department of Computer Science, 4 Center for Medical Informatics and 5 Department of Genetics, Yale University, New Haven, CT 06520, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,6,1]]},"reference":[{"key":"2023012508070409300_B1","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1038\/nrg1895","article-title":"Primate segmental duplications: crucibles of evolution, diversity and disease","volume":"7","author":"Bailey","year":"2006","journal-title":"Nat. Rev. Genet."},{"key":"2023012508070409300_B2","first-page":"659","article-title":"Cooking the semantic web with the OWL API","volume-title":"ISWC 2003","author":"Bechhofer","year":"2003"},{"key":"2023012508070409300_B3","article-title":"A probabilistic extension to ontology language owl","volume-title":"Proceedings of the 37th Hawaii International Conference On System Sciences (HICSS-37)","author":"Ding","year":"2004"},{"key":"2023012508070409300_B4","author":"Duplication,S.","year":"2010"},{"key":"2023012508070409300_B5","doi-asserted-by":"crossref","first-page":"642","DOI":"10.1002\/cfg.446","article-title":"Sequence ontology annotation guide","volume":"5","author":"Eilbeck","year":"2004","journal-title":"Comp. Funct. 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