{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T14:20:01Z","timestamp":1790086801563,"version":"4.0.1"},"reference-count":80,"publisher":"SAGE Publications","license":[{"start":{"date-parts":[[2009,1,1]],"date-time":"2009-01-01T00:00:00Z","timestamp":1230768000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Evol Bioinform Online"],"published-print":{"date-parts":[[2009,1]]},"abstract":"<jats:p>Comparative analysis is used throughout biology. When entities under comparison (e.g. proteins, genomes, species) are related by descent, evolutionary theory provides a framework that, in principle, allows N-ary comparisons of entities, while controlling for non-independence due to relatedness. Powerful software tools exist for specialized applications of this approach, yet it remains under-utilized in the absence of a unifying informatics infrastructure. A key step in developing such an infrastructure is the definition of a formal ontology. The analysis of use cases and existing formalisms suggests that a significant component of evolutionary analysis involves a core problem of inferring a character history, relying on key concepts: \u201cOperational Taxonomic Units\u201d (OTUs), representing the entities to be compared; \u201ccharacter-state data\u201d representing the observations compared among OTUs; \u201cphylogenetic tree\u201d, representing the historical path of evolution among the entities; and \u201ctransitions\u201d, the inferred evolutionary changes in states of characters that account for observations. Using the Web Ontology Language (OWL), we have defined these and other fundamental concepts in a Comparative Data Analysis Ontology (CDAO). CDAO has been evaluated for its ability to represent token data sets and to support simple forms of reasoning. With further development, CDAO will provide a basis for tools (for semantic transformation, data retrieval, validation, integration, etc.) that make it easier for software developers and biomedical researchers to apply evolutionary methods of inference to diverse types of data, so as to integrate this powerful framework for reasoning into their research.<\/jats:p>","DOI":"10.4137\/ebo.s2320","type":"journal-article","created":{"date-parts":[[2017,11,9]],"date-time":"2017-11-09T06:00:07Z","timestamp":1510207207000},"source":"Crossref","is-referenced-by-count":18,"title":["Initial Implementation of a Comparative Data Analysis Ontology"],"prefix":"10.4137","volume":"5","author":[{"given":"Francisco","family":"Prosdocimi","sequence":"first","affiliation":[{"name":"Department of Structural Biology and Genomics, Institut de G\u00e9n\u00e9tique et de Biologie mol\u00e9culaire et Cellulaire (IGBMC), F-67400 Illkirch, France; Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale (INSERM), U964, F-67400 Illkirch, France; the Centre National de la Recherche Scientifique (CNRS), UMR7104, F-67400 Illkirch, France; Universit\u00e9 de Strasbourg, F-67000 Strasbourg, France."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brandon","family":"Chisham","sequence":"additional","affiliation":[{"name":"Department of Computer Science, New Mexico State University, P.O. Box 30001, MSC CS, Las Cruces, NM 88003, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Enrico","family":"Pontelli","sequence":"additional","affiliation":[{"name":"Department of Computer Science, New Mexico State University, P.O. Box 30001, MSC CS, Las Cruces, NM 88003, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julie D.","family":"Thompson","sequence":"additional","affiliation":[{"name":"Department of Structural Biology and Genomics, Institut de G\u00e9n\u00e9tique et de Biologie mol\u00e9culaire et Cellulaire (IGBMC), F-67400 Illkirch, France; Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale (INSERM), U964, F-67400 Illkirch, France; the Centre National de la Recherche Scientifique (CNRS), UMR7104, F-67400 Illkirch, France; Universit\u00e9 de Strasbourg, F-67000 Strasbourg, France."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arlin","family":"Stoltzfus","sequence":"additional","affiliation":[{"name":"Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky drive, Rockville, Maryland 20850, USA; Biochemical Science division, National Institute of Standards and Technology, Mail Stop 8310, 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