Initial implementation of a comparative data analysis ontology. Export

@article{citeulike:5922761, 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.}, author = {Prosdocimi, Francisco and Chisham, Brandon and Pontelli, Enrico and Thompson, Julie D. and Stoltzfus, Arlin}, citeulike-article-id = {5922761}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/19812726}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=19812726}, issn = {1176-9343}, journal = {Evolutionary bioinformatics online}, keywords = {biology}, pages = {47--66}, posted-at = {2009-10-11 23:03:08}, priority = {2}, title = {Initial implementation of a comparative data analysis ontology.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/19812726}, volume = {5}, year = {2009} }

TY - JOUR ID - citeulike:5922761 L3 - citeulike-article-id:5922761 N2 - 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. JF - Evolutionary bioinformatics online SN - 1176-9343 EP - 66 TI - Initial implementation of a comparative data analysis ontology. VL - 5 SP - 47 KW - biology AU - Prosdocimi, Francisco AU - Chisham, Brandon AU - Pontelli, Enrico AU - Thompson, Julie AU - Stoltzfus, Arlin PY - 2009/// UR - http://view.ncbi.nlm.nih.gov/pubmed/19812726 ER -