Difference between revisions of "Ontologies"

From phenoscape
Jump to: navigation, search
(On the web)
(Taxonomy Ontology)
Line 3: Line 3:
 
== Taxonomy Ontology ==
 
== Taxonomy Ontology ==
  
Phenotypes are associated with species using a taxonomy ontology, the [http://bioportal.bioontology.org/visualize/38363 Teleost Taxonomy Ontology (TTO)] derived from the [http://www.calacademy.org/RESEARCH/ichthyology/catalog/fishcatsearch.html Catalog of Fishes].
+
Phenotypes are associated with species using a taxonomy ontology, the [http://bioportal.bioontology.org/visualize/38363 Teleost Taxonomy Ontology (TTO)] derived from the [http://www.calacademy.org/RESEARCH/ichthyology/catalog/fishcatsearch.html Catalog of Fishes]. The TTO is updated in concert with Catalog of Fishes updates.  Changes to the TTO relative to the latest version generated from a dump from the Catalog of Fishes are documented [[TTO_Changes]].
 
+
There is now a page of [[TTO_Changes]] relative to the latest version generated from a dump from the Catalog of Fishes.
+
  
 
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.

Revision as of 15:29, 22 October 2008

Evolutionary phenotypes are being 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 are associated with species using a taxonomy ontology, the Teleost Taxonomy Ontology (TTO) derived from the Catalog of Fishes. The TTO is updated in concert with Catalog of Fishes updates. Changes to the TTO relative to the latest version generated from a dump from the Catalog of Fishes are documented TTO_Changes.

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.

Fish Collection Codes

There is a vocabulary of fish collections, based on a list used in Catalog of Fishes, though with a few additions listed on the Fish Collection Updates page.

The current release, as used in Phenex is Fish Collection Abbreviations

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.

Viewing ontologies

Click on the "Visualization" tab to browse the ontologies graphically.


On your desktop

Ontologies can be downloaded as OBO files from the above web sites, and viewed on your desktop using the OBO-Edit desktop software.