Difference between revisions of "Ontologies"
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Evolutionary phenotypes will be described using the [http://www.bioontology.org/wiki/index.php/PATO:About Entity-Quality system], which combines morphological terms from an anatomical ontology (here: the Teleost Anatomy Ontology, TAO) with quality terms from the [http://www.bioontology.org/wiki/index.php/PATO:Main_Page Phenotype and Trait Ontology (PATO)]. | Evolutionary phenotypes will be described using the [http://www.bioontology.org/wiki/index.php/PATO:About Entity-Quality system], which combines morphological terms from an anatomical ontology (here: the Teleost Anatomy Ontology, TAO) with quality terms from the [http://www.bioontology.org/wiki/index.php/PATO:Main_Page Phenotype and Trait Ontology (PATO)]. | ||
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| + | == Taxonomy Ontology == | ||
Phenotypes will be associated with taxa using a [[taxonomy ontology]] derived from the [http://www.calacademy.org/RESEARCH/ichthyology/catalog/fishcatsearch.html Catalog of Fishes], the Teleost Taxonomy Ontology (TTO). | Phenotypes will be associated with taxa using a [[taxonomy ontology]] derived from the [http://www.calacademy.org/RESEARCH/ichthyology/catalog/fishcatsearch.html Catalog of Fishes], the Teleost Taxonomy Ontology (TTO). | ||
We are in the process of developing a separate ontology of [[Taxonomic Ranks]]. These terms (e.g., family, genus, etc.) will then be removed from the TTO and links from taxonomic terms (property_value: has_rank) will be updated. | We are in the process of developing a separate ontology of [[Taxonomic Ranks]]. These terms (e.g., family, genus, etc.) will then be removed from the TTO and links from taxonomic terms (property_value: has_rank) will be updated. | ||
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| + | == Anatomy Ontology == | ||
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| + | The Teleost Anatomy Ontology (TAO) is a multi-species ontology and was initialized with the terms in the Zebrafish Anatomical Ontology (ZFA). The development of the TAO currently focuses on the skeletal system because it varies significantly across the Ostariophysi, is well-preserved in fossil specimens, and it is often the focus of morphologically-based evolutionary studies in ichthyology. | ||
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| + | == OBO Repository Deposition == | ||
Although the anatomy as well as the taxonomy ontologies will keep changing to accommodate our curation needs, both have been admitted into the OBO CVS-based version-control system, from where the NCBO's BioPortal loads and updates ontologies on a regular basis. Both [http://www.bioontology.org/ncbo/faces/pages/ontology_details.xhtml?ontology_display_name=Teleost%20anatomy%20and%20development%20(TAO) TAO] and [http://www.bioontology.org/ncbo/faces/pages/ontology_details.xhtml?ontology_display_name=Teleost%20taxonomy TTO] can be browsed, searched, and visualized at the NCBO BioPortal. | Although the anatomy as well as the taxonomy ontologies will keep changing to accommodate our curation needs, both have been admitted into the OBO CVS-based version-control system, from where the NCBO's BioPortal loads and updates ontologies on a regular basis. Both [http://www.bioontology.org/ncbo/faces/pages/ontology_details.xhtml?ontology_display_name=Teleost%20anatomy%20and%20development%20(TAO) TAO] and [http://www.bioontology.org/ncbo/faces/pages/ontology_details.xhtml?ontology_display_name=Teleost%20taxonomy TTO] can be browsed, searched, and visualized at the NCBO BioPortal. | ||
Revision as of 21:40, 29 April 2008
Evolutionary phenotypes will be described using the Entity-Quality system, which combines morphological terms from an anatomical ontology (here: the Teleost Anatomy Ontology, TAO) with quality terms from the Phenotype and Trait Ontology (PATO).
Taxonomy Ontology
Phenotypes will be associated with taxa using a taxonomy ontology derived from the Catalog of Fishes, the Teleost Taxonomy Ontology (TTO).
We are in the process of developing a separate ontology of Taxonomic Ranks. These terms (e.g., family, genus, etc.) will then be removed from the TTO and links from taxonomic terms (property_value: has_rank) will be updated.
Anatomy Ontology
The Teleost Anatomy Ontology (TAO) is a multi-species ontology and was initialized with the terms in the Zebrafish Anatomical Ontology (ZFA). The development of the TAO currently focuses on the skeletal system because it varies significantly across the Ostariophysi, is well-preserved in fossil specimens, and it is often the focus of morphologically-based evolutionary studies in ichthyology.
OBO Repository Deposition
Although the anatomy as well as the taxonomy ontologies will keep changing to accommodate our curation needs, both have been admitted into the OBO CVS-based version-control system, from where the NCBO's BioPortal loads and updates ontologies on a regular basis. Both TAO and TTO can be browsed, searched, and visualized at the NCBO BioPortal.
