Ontologies
Phenoscape is using multiple ontologies to describe variation in phenotypes across species. We have developed several new ontologies required for evolutionary biology, but whenever possible, we are sharing existing ontologies with the broader biological community. This will ensure the greatest interoperability between evolutionary and model organism data.
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.
These ontologies will keep changing to accommodate our community needs, and they 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.
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. Details about the taxonomy ontology can also be found here.
Documenting taxon concepts used in a publication
Taxonomy ontology: ranks, unknown/unnamed species, & related issues
Ambiguous specimen information: annotating phenotypes for specimens or species
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. Details about the development of the TAO can be found here.
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
Evidence Code Ontology
Relations Ontology
Spatial Ontology
Comparative Data Analysis Ontology
CDAO is developed by the EvoInfo working group at NESCent, and is being used within the Phenoscape OBD data repository.
