{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,13]],"date-time":"2026-03-13T23:29:59Z","timestamp":1773444599177,"version":"3.50.1"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":3015,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: The classification of biological entities in terms of species and taxa is an important endeavor in biology. Although a large amount of statements encoded in current biomedical ontologies is taxon-dependent there is no obvious or standard way for introducing taxon information into an integrative ontology architecture, supposedly because of ongoing controversies about the ontological nature of species and taxa.<\/jats:p><jats:p>Results: In this article, we discuss different approaches on how to represent biological taxa using existing standards for biomedical ontologies such as the description logic OWL DL and the Open Biomedical Ontologies Relation Ontology. We demonstrate how hidden ambiguities of the species concept can be dealt with and existing controversies can be overcome. A novel approach is to envisage taxon information as qualities that inhere in biological organisms, organism parts and populations.<\/jats:p><jats:p>Availability: The presented methodology has been implemented in the domain top-level ontology BioTop, openly accessible at http:\/\/purl.org\/biotop. BioTop may help to improve the logical and ontological rigor of biomedical ontologies and further provides a clear architectural principle to deal with biological taxa information.<\/jats:p><jats:p>Contact: \u00a0stschulz@uni-freiburg.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn158","type":"journal-article","created":{"date-parts":[[2008,6,27]],"date-time":"2008-06-27T07:43:13Z","timestamp":1214552593000},"page":"i313-i321","source":"Crossref","is-referenced-by-count":23,"title":["The ontology of biological taxa"],"prefix":"10.1093","volume":"24","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, Germany and 2Digital Enterprise Research Institute (DERI), National University of Ireland, Galway, University Road, Galway, Ireland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Holger","family":"Stenzhorn","sequence":"additional","affiliation":[{"name":"1 Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Stefan-Meier-Str. 26, 79104 Freiburg, Germany and 2Digital Enterprise Research Institute (DERI), National University of Ireland, Galway, University Road, Galway, Ireland"},{"name":"1 Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Stefan-Meier-Str. 26, 79104 Freiburg, Germany and 2Digital Enterprise Research Institute (DERI), National University of Ireland, Galway, University Road, Galway, Ireland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Boeker","sequence":"additional","affiliation":[{"name":"1 Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Stefan-Meier-Str. 26, 79104 Freiburg, Germany and 2Digital Enterprise Research Institute (DERI), National University of Ireland, Galway, University Road, Galway, Ireland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,7,1]]},"reference":[{"key":"2023020210411338500_B1","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. Gene ontology consortium","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet"},{"key":"2023020210411338500_B2","article-title":"The Description Logic Handbook","volume-title":"Theory, Implementation, and Applications","author":"Baader","year":"2003"},{"key":"2023020210411338500_B3","first-page":"37","article-title":"Individuals, universals, collections: on the foundational relations of ontology. In","volume-title":"Formal Ontology in Information Systems","author":"Bittner","year":"2004"},{"key":"2023020210411338500_B4","doi-asserted-by":"crossref","first-page":"141","DOI":"10.7551\/mitpress\/6396.003.0012","article-title":"Homeostasis, species, and higher taxa. In","volume-title":"Species: New Interdisciplinary Essays","author":"Boyd","year":"1999"},{"key":"2023020210411338500_B5","article-title":"On the origin of species. In","volume-title":"The Works of Charles Darwin","author":"Darwin","year":"1859"},{"key":"2023020210411338500_B6","volume-title":"The Poverty of the Linnaean Hierarchy: A Philosophical Study of Biological Taxonomy","author":"Ereshefsky","year":"2001"},{"key":"2023020210411338500_B7","unstructured":"Ereshefsky M Zalta N Species. The Stanford Encyclopedia of Philosophy. In 2007 last accessed date January 11, 2008 (Summer 2007 edition) http:\/\/plato.stanford.edu\/archives\/sum2007\/entries\/species"},{"key":"2023020210411338500_B8","first-page":"26","author":"Gangemi","year":"2001"},{"key":"2023020210411338500_B9","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1007\/3-540-45810-7_18","article-title":"Sweetening ontologies with Dolce. In:","volume-title":"Knowledge Engineering and Knowledge Management: Ontologies and the Semantic Web","author":"Gangemi","year":"2002"},{"key":"2023020210411338500_B10","doi-asserted-by":"crossref","first-page":"536","DOI":"10.2307\/2412471","article-title":"A radical solution to the species problem","volume":"23","author":"Ghiselin","year":"1974","journal-title":"Syst. Zool."},{"key":"2023020210411338500_B11","volume-title":"The Structure of Appearance","author":"Goodman","year":"1951"},{"key":"2023020210411338500_B12","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511819018","volume-title":"The Philosophy of Biology: An Episodic History","author":"Grene","year":"2004"},{"key":"2023020210411338500_B13","first-page":"3","volume-title":"Formal Ontology in Information Systems","author":"Guarino","year":"1998"},{"key":"2023020210411338500_B14","first-page":"25","article-title":"Ontologies and knowledge bases: towards a terminological clarification. In","volume-title":"Towards Very Large Knowledge Bases: Knowledge Building and Knowledge Sharing","author":"Guarino","year":"1998"},{"key":"2023020210411338500_B15","first-page":"57","article-title":"Ontological Categories in GOL","volume-title":"Axiomathes","author":"Heller","year":"2004"},{"key":"2023020210411338500_B16","volume-title":"Phylogenetic Systematics","author":"Hennig","year":"1966"},{"key":"2023020210411338500_B17","first-page":"447","article-title":"On the failure of modern species concepts","volume-title":"Trends Ecol. Evol","author":"Hey","year":"2006"},{"key":"2023020210411338500_B18","first-page":"314","article-title":"The effect of essentialism on taxonomy: two thousand years of stasis","volume-title":"Br. J. Philos. Sci.","author":"Hull","year":"1965"},{"key":"2023020210411338500_B19","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1086\/288811","article-title":"A matter of individuality","volume":"45","author":"Hull","year":"1978","journal-title":"Philos. Sci."},{"key":"2023020210411338500_B20","first-page":"357","article-title":"The ideal species concept \u2013 and why we cannot get it. In","volume-title":"Species: The Units of Biodiversity","author":"Hull","year":"1997"},{"key":"2023020210411338500_B21","author":"International Organization for Standardization (ISO)","year":"2000"},{"key":"2023020210411338500_B22","first-page":"39","article-title":"Nontological Engineering. Formal Ontology In Information Systems.","volume-title":"Proceedings of the 4th International Conference FOIS 2006","author":"Ku\u015bnierczyk","year":"2006"},{"key":"2023020210411338500_B23","unstructured":"Masolo C \u00a0et al. WonderWeb Deliverable D18 Ontology Library Infrastructure for the Semantic Web 2003 last accessed date January 11, 2008 http:\/\/wonderweb.semanticweb.org"},{"key":"2023020210411338500_B24","first-page":"381","article-title":"A hierarchy of species concepts: the denouement of the species problem. In:","volume-title":"Species: The Units of Biodiversity","author":"Mayden","year":"1997"},{"key":"2023020210411338500_B25","volume-title":"Systematics and the Origin of Species","author":"Mayr","year":"1942"},{"key":"2023020210411338500_B26","volume-title":"Principles of Systematic Zoology","author":"Mayr","year":"1969"},{"key":"2023020210411338500_B27","first-page":"73","article-title":"GENIA Corpus: an annotated research abstract corpus in molecular biology domain.","volume-title":"Proceedings of the Human Language Technology Conference (HLT 2002)","author":"Ohta","year":"2002"},{"key":"2023020210411338500_B28","author":"Quine","year":"1948"},{"key":"2023020210411338500_B29","first-page":"333","article-title":"Granularity, scale and collectivity: when size does and does not matter","volume-title":"J. Biomed. Informatics","author":"Rector","year":"2006"},{"key":"2023020210411338500_B30","unstructured":"Rector A \u00a0et al. Simple Bio Upper Ontology 2007 last accessed date January 15, 2008 [http:\/\/www.cs.man.ac.uk\/~rector\/ontologies\/simple-top-bio]"},{"key":"2023020210411338500_B31","first-page":"75","article-title":"Biomedical ontologies: a functional perspective","volume-title":"Brief. Bioinform.","author":"Rubin","year":"2008"},{"key":"2023020210411338500_B32","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1016\/j.jbi.2005.11.003","article-title":"Biomedical ontologies: what part-of is and isn't","volume":"39","author":"Schulz","year":"2006","journal-title":"J. Biomed. Inform"},{"key":"2023020210411338500_B33","first-page":"103","author":"Schulz","year":"2006"},{"key":"2023020210411338500_B34","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1016\/j.artmed.2006.12.001","article-title":". Towards the ontological foundations of symbolic biological theories","volume":"39","author":"Schulz","year":"2007","journal-title":"Artif. Intell. Med"},{"key":"2023020210411338500_B35","doi-asserted-by":"crossref","DOI":"10.5840\/monist200790434","article-title":"Continua in biological systems","author":"Schulz","year":"2007"},{"key":"2023020210411338500_B36","doi-asserted-by":"crossref","DOI":"10.7312\/simp92414","article-title":"Principles of Animal Taxonomy","author":"Simpson","year":"1961"},{"key":"2023020210411338500_B37","first-page":"R46","article-title":"Relations in biomedical ontologies.","volume-title":"Genome Biol","author":"Smith","year":"2005"},{"key":"2023020210411338500_B38","doi-asserted-by":"crossref","first-page":"1251","DOI":"10.1038\/nbt1346","article-title":"The OBO foundry: coordinated evolution of ontologies to support biomedical data integration","volume":"25","author":"Smith","year":"2007","journal-title":"Nat. Biotechnol"},{"key":"2023020210411338500_B39","first-page":"1225","article-title":"Towards a top \u2013 domain ontology for linking biomedical ontologies. In:","volume-title":"MEDINFO 2007 \u2013 Proceedings of the 12th World Congress on Health (Medical) Informatics \u2013 Building Sustainable Health Systems","author":"Stenzhorn","year":"2007"},{"key":"2023020210411338500_B40","doi-asserted-by":"crossref","first-page":"D13","DOI":"10.1093\/nar\/gkm1000","article-title":"Database resources of the national center for biotechnology information","volume":"36","author":"Wheeler","year":"2008","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/13\/i313\/49054268\/bioinformatics_24_13_i313.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/13\/i313\/49054268\/bioinformatics_24_13_i313.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,27]],"date-time":"2024-02-27T22:21:45Z","timestamp":1709072505000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/13\/i313\/231125"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,7,1]]},"references-count":40,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2008,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn158","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,7,1]]},"published":{"date-parts":[[2008,7,1]]}}}