Skip to Main content Skip to Navigation
Journal articles

Initial implementation of a comparative data analysis ontology.

Abstract : 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: "Operational Taxonomic Units" (OTUs), representing the entities to be compared; "character-state data" representing the observations compared among OTUs; "phylogenetic tree", representing the historical path of evolution among the entities; and "transitions", 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.
Complete list of metadata
Contributor : Maité Peney Connect in order to contact the contributor
Submitted on : Tuesday, December 8, 2009 - 7:48:27 PM
Last modification on : Friday, December 3, 2021 - 9:00:06 AM
Long-term archiving on: : Thursday, June 17, 2010 - 11:10:25 PM


Publisher files allowed on an open archive


  • HAL Id : inserm-00438663, version 1
  • PUBMED : 19812726



Francisco Prosdocimi, Brandon Chisham, Enrico Pontelli, Julie D. Thompson, Arlin Stoltzfus. Initial implementation of a comparative data analysis ontology.. Evolutionary Bioinformatics, Libertas Academica (New Zealand), 2009, 5, pp.47-66. ⟨inserm-00438663⟩



Record views


Files downloads