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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

Annotation of rooted and unrooted evolutionary trees using CDAO concepts and relations. a) An example of a rooted tree showing how the concepts and relations defined in CDAO can be used to represent the topology of the tree and associated data. In particular, important evolutionary concepts, such as the Most Recent Common Ancestor (MRCA) can be specified. In the case of a rooted tree, the edges (or branches) of the tree are directed and the relations has_parent_node and has_child_node are used. b) The representation of an unrooted tree using CDAO. here, the direction of the edges is unknown and the relations has_Left_node and has_Right_node are used. Unrooted trees may contain subtrees for which the ancestor node is known, and in this case a rooted subtree can be specified using the has_Root relation.
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f4-ebo-2009-047: Annotation of rooted and unrooted evolutionary trees using CDAO concepts and relations. a) An example of a rooted tree showing how the concepts and relations defined in CDAO can be used to represent the topology of the tree and associated data. In particular, important evolutionary concepts, such as the Most Recent Common Ancestor (MRCA) can be specified. In the case of a rooted tree, the edges (or branches) of the tree are directed and the relations has_parent_node and has_child_node are used. b) The representation of an unrooted tree using CDAO. here, the direction of the edges is unknown and the relations has_Left_node and has_Right_node are used. Unrooted trees may contain subtrees for which the ancestor node is known, and in this case a rooted subtree can be specified using the has_Root relation.

Mentions: In CDAO, phylogenetic trees and networks are made of Nodes and Edges (Fig. 4). A Node may be linked by the represents_TU property to a TU, which represents a biological entity subject to evolutionary changes in its Characters. An Edge represents the connection between two nodes in a tree or a network; it is described by the property has_Node, which associates the edge to the nodes it connects, i.e.


Initial implementation of a comparative data analysis ontology.

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

Annotation of rooted and unrooted evolutionary trees using CDAO concepts and relations. a) An example of a rooted tree showing how the concepts and relations defined in CDAO can be used to represent the topology of the tree and associated data. In particular, important evolutionary concepts, such as the Most Recent Common Ancestor (MRCA) can be specified. In the case of a rooted tree, the edges (or branches) of the tree are directed and the relations has_parent_node and has_child_node are used. b) The representation of an unrooted tree using CDAO. here, the direction of the edges is unknown and the relations has_Left_node and has_Right_node are used. Unrooted trees may contain subtrees for which the ancestor node is known, and in this case a rooted subtree can be specified using the has_Root relation.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f4-ebo-2009-047: Annotation of rooted and unrooted evolutionary trees using CDAO concepts and relations. a) An example of a rooted tree showing how the concepts and relations defined in CDAO can be used to represent the topology of the tree and associated data. In particular, important evolutionary concepts, such as the Most Recent Common Ancestor (MRCA) can be specified. In the case of a rooted tree, the edges (or branches) of the tree are directed and the relations has_parent_node and has_child_node are used. b) The representation of an unrooted tree using CDAO. here, the direction of the edges is unknown and the relations has_Left_node and has_Right_node are used. Unrooted trees may contain subtrees for which the ancestor node is known, and in this case a rooted subtree can be specified using the has_Root relation.
Mentions: In CDAO, phylogenetic trees and networks are made of Nodes and Edges (Fig. 4). A Node may be linked by the represents_TU property to a TU, which represents a biological entity subject to evolutionary changes in its Characters. An Edge represents the connection between two nodes in a tree or a network; it is described by the property has_Node, which associates the edge to the nodes it connects, i.e.

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