Difference between revisions of "Individual-based taxonomy"
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Representing evolutionary lineages using ontological individuals has some modeling advantages, and may be more realistic, compared with using a simple class hierarchy. We described some of the rationale in [http://ceur-ws.org/Vol-833/paper82.pdf these ICBO conference proceedings]. For the purposes of the Phenoscape KB, this model supports specification of the [[Semantics_of_phenotype_annotations|semantics of particular phenotype annotations]]: the phenotype applies to all members of a clade, is observed for some members, or is applied to the ancestor of the members. | Representing evolutionary lineages using ontological individuals has some modeling advantages, and may be more realistic, compared with using a simple class hierarchy. We described some of the rationale in [http://ceur-ws.org/Vol-833/paper82.pdf these ICBO conference proceedings]. For the purposes of the Phenoscape KB, this model supports specification of the [[Semantics_of_phenotype_annotations|semantics of particular phenotype annotations]]: the phenotype applies to all members of a clade, is observed for some members, or is applied to the ancestor of the members. | ||
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| + | In the KB build process, the VTO taxon class hierarchy is translated into a relationship graph. For every class relationships such as: | ||
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| + | Class: Ictaluridae | ||
| + | SubClassOf: Siluriformes | ||
| + | |||
| + | Individuals with the same IDs (using OWL punning) are created with a relationship such as: | ||
| + | |||
| + | Individual: Ictaluridae | ||
| + | Facts: subCladeOf Siluriformes | ||
[[Category:Reasoning]] | [[Category:Reasoning]] | ||
[[Category:Ontology]] | [[Category:Ontology]] | ||
Revision as of 18:00, 8 July 2013
Representing evolutionary lineages using ontological individuals has some modeling advantages, and may be more realistic, compared with using a simple class hierarchy. We described some of the rationale in these ICBO conference proceedings. For the purposes of the Phenoscape KB, this model supports specification of the semantics of particular phenotype annotations: the phenotype applies to all members of a clade, is observed for some members, or is applied to the ancestor of the members.
In the KB build process, the VTO taxon class hierarchy is translated into a relationship graph. For every class relationships such as:
Class: Ictaluridae
SubClassOf: Siluriformes
Individuals with the same IDs (using OWL punning) are created with a relationship such as:
Individual: Ictaluridae
Facts: subCladeOf Siluriformes
