Ontologies
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).
Contents
New Ontologies
Phenoscape has developed ontologies that are required for the annotation of evolutionary phenotypes in fishes. These ontologies are publicly available and being used by the community.
Teleost 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.
Teleost Anatomy Ontology
The Teleost Anatomy Ontology (TAO) is a multi-species ontology that 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 Ontology
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
Existing Ontologies
These ontologies were developed and shared by a variety of model organism communities. Phenoscape is involved in extending these ontologies.
Phenotype and Trait Ontology (PATO)
Evidence Code Ontology
Relations Ontology
Spatial Ontology
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.
