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.

Ontologies Initiated by Phenoscape

Phenoscape has developed ontologies that are required for the annotation of evolutionary phenotypes in fishes. These ontologies are publicly available and being used and extended by the community (view the list of contributors).

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. Ontologies available at the BioPortal can be browsed, searched, and visualized at the NCBO BioPortal. Ontologies are also available for download as .obo files from the BioPortal or OBO Foundry, and viewed using the OBO-Edit desktop software.

Anatomy Ontologies

Teleost Anatomy Ontology

The Teleost Anatomy Ontology (TAO) is a multi-species ontology that was initialized with terms from the Zebrafish Anatomical Ontology (ZFA). The development of the TAO currently focuses on the skeletal system because it varies significantly across fishes, 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.

• Browse TAO at BioPortal
• Download TAO from Bioportal or OBO Foundry (use OBO Edit desktop software to open and view .obo file).

Version X, Target release date: Late August 2011

- High-level skeletal terms from VAO will be imported into TAO with the next release

Vertebrate Anatomy Ontology

Release Schedule and Features

Version X, Target release date: Late August 2011

- New skeletal terms for the limb/fin and cranial skeleton will be added based on work done at the Phenotype RCN Vertebrate Working Group meeting.

- Terms from external ontologies (GO, PATO, Cell) will be imported by MIREOT

- New term request page at Sourceforge will be set up

Amniote Anatomy Ontology

Version X, Target release date: Late August 2011

- VAO terms will be imported

- Taxon restrictions for chick terms will be implemented

- All terms will be defined

Taxonomy Ontologies

Teleost Taxonomy Ontology

Phenotypes are associated with species using a taxonomy ontology, the Teleost Taxonomy Ontology (TTO) derived from the Catalog of Fishes (see also the representation on BioPortal, which can be navigated on-line). 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.

Taxonomic Rank Vocabulary

During 2010, we released a separate Taxonomic Rank Vocabulary (TAXRANK), and removed all rank terms (e.g., family, genus, etc.) from the taxa within the TTO. Taxa in the TTO specify their ranks as property values via the metadata relation has_rank, but the object of the has_rank links is contained in the TAXRANK vocabulary.

Developing TAXRANK as a vocabulary, rather than an ontology (e.g., by defining an ordering relation between ranks) should facilitate its reuse in other taxonomic ontologies. Developing a cross-authority (e.g., ICZN, ICBN, etc.) ontology of ranks may be possible, but there does not appear to be a compelling need for such an ontology.

Additional documentation:

• Documenting taxon concepts used in a publication
• Taxonomy ontology: ranks, unknown/unnamed species, & related issues
• Ambiguous specimen information: annotating phenotypes for specimens or species (also called the Hypodigm problem)

• Browse TTO at BioPortal
• Download TTO from Bioportal or OBO Foundry (use OBO Edit desktop software to open and view .obo file).

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. It has been augmented with links to entries in the Biodiversity Collections Index.

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

Shared Ontologies

These ontologies listed below were initiated by the model organism communities. Phenoscape is actively involved in extending these ontologies.

Phenotype and Trait Ontology

• Phenotype and Trait Ontology (PATO)

Evidence Code Ontology

• Evidence Code Ontology

Relations Ontology

• OBO-relations

Spatial 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.

• CDAO