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Initial implementation of a comparative data analysis ontology.

Prosdocimi F, Chisham B, Pontelli E, Thompson JD, Stoltzfus A - Evol. Bioinform. Online (2009)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Structural Biology and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), F-67400 Illkirch, France.

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.

No MeSH data available.


Related in: MedlinePlus

Some key concepts and relations formalized in CDAO. Domain-specific terms in CDAO represent either classes, shown by ovals and boxes, or properties (also called “relations”), shown by lines with arrows. The subsumption property “is_a” relates a class to its superclass (solid lines). other properties are defined in CDAO and discussed in the text (dashed lines).
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f3-ebo-2009-047: Some key concepts and relations formalized in CDAO. Domain-specific terms in CDAO represent either classes, shown by ovals and boxes, or properties (also called “relations”), shown by lines with arrows. The subsumption property “is_a” relates a class to its superclass (solid lines). other properties are defined in CDAO and discussed in the text (dashed lines).

Mentions: The key concepts for the core problem of evolutionary character analysis include character-state data, OTUs, phylogenies, and transitions. Except for “transitions”, which for the present are represented as annotations of tree branches, these concepts have been implemented as separate class hierarchies in CDAO (Fig. 3), with a minimal number of relationships linking important concepts in each hierarchy. Each of these hierarchies is described in the rest of this section.


Initial implementation of a comparative data analysis ontology.

Prosdocimi F, Chisham B, Pontelli E, Thompson JD, Stoltzfus A - Evol. Bioinform. Online (2009)

Some key concepts and relations formalized in CDAO. Domain-specific terms in CDAO represent either classes, shown by ovals and boxes, or properties (also called “relations”), shown by lines with arrows. The subsumption property “is_a” relates a class to its superclass (solid lines). other properties are defined in CDAO and discussed in the text (dashed lines).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2747124&req=5

f3-ebo-2009-047: Some key concepts and relations formalized in CDAO. Domain-specific terms in CDAO represent either classes, shown by ovals and boxes, or properties (also called “relations”), shown by lines with arrows. The subsumption property “is_a” relates a class to its superclass (solid lines). other properties are defined in CDAO and discussed in the text (dashed lines).
Mentions: The key concepts for the core problem of evolutionary character analysis include character-state data, OTUs, phylogenies, and transitions. Except for “transitions”, which for the present are represented as annotations of tree branches, these concepts have been implemented as separate class hierarchies in CDAO (Fig. 3), with a minimal number of relationships linking important concepts in each hierarchy. Each of these hierarchies is described in the rest of this section.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Structural Biology and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), F-67400 Illkirch, France.

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.

No MeSH data available.


Related in: MedlinePlus