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 several ontologies (TAO, VAO, TTO) that are required for the annotation of evolutionary phenotypes across species. 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. 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

Phenoscape is coordinating the integration of model organism (zebrafish, Xenopus, mouse) and multi-species (teleost, amphibian, amniote) anatomy ontologies for vertebrates. The development plan and release schedule for these anatomy ontologies detail the working plan for their integration. We hold a weekly project anatomy ontology conference call to discuss development with the curators of these ontologies.

Vertebrate anatomy term tracker

Ontology update requests can be made on the Vertebrate Anatomy term request tracker. Requests are forwarded to the vertebrate anatomy mailing list.

• Submit term requests to the vertebrate anatomy request tracker

• Subscribe to the vertebrate anatomy mailing list for notification of term requests

Anatomy mailing list

Discussion of vertebrate and general anatomy issues are posted to the obo-anatomy list:

• Subscribe or view list archives here: obo-anatomy mailing list

• View obo-anatomy list archives

Vertebrate Anatomy Ontology

VAO contains terms representing structures in the musculo-skeletal system of vertebrates. It imports terms from the Common Anatomy Reference Ontology (CARO). VAO can be downloaded at the OBO Foundry and browsed at BioPortal.

Teleost Anatomy Ontology

TAO is a multi-species ontology for teleost fishes 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. The development of the TAO is described in Dahdul et al. (2010). Download TAO from the OBO Foundry and browse at BioPortal

Amphibian Anatomy Ontology

AAO is a multispecies ontology for amphibian anatomy. It will be used to annotate characters from the amphibian systematics literature. Download AAO from the OBO Foundry and browse at BioPortal

Amniote Anatomy Ontology

AMAO is a new anatomy ontology being developed for amniotes. It will import skeletal terms from VAO and non-skeletal terms from Uberon.

Zebrafish Anatomical Ontology

ZFA is used by ZFIN to annotate mutant phenotypes for the model organsim zebrafish (Danio rerio). ZFA can be downloaded from the OBO Foundry and browsed at the BioPortal.

Xenopus Anatomy Ontology

XAO contains terms that represent anatomical structures for the model organism Xenopus laevis (African clawed frog). Xenbase uses XAO to annotate Xenopus gene expression and phenotypes. XAO can be downloaded at the OBO Foundry and browsed at the BioPortal.

Mouse Adult Gross Anatomy

MA contains terms that represent structures in the adult mouse (Mus) and is used to annotate gene expression and phenotypes for mouse at Mouse Genome Informatics (MGI). Download MA at the OBO Foundry and browse the ontology at the BioPortal.

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.

Amphibian Taxonomy Ontology

The ATO is derived from the AmphibiaWeb list, which provides both taxonomy and some synonyms from ITIS and the IUCN redlist.

Vertebrate Taxonomy Ontology

The Vertebrate Taxonomy Ontology includes the TTO, ATO, as well as a new Amniote Taxonomy Ontology. An initial release, including TTO and ATO, but using pan-vertebrate resources (see below) rather than a separate AmTO was made in May 2011. This taxonomy covers vertebrates and was built by starting with the NCBI taxonomy for vertebrates and splicing in TTO (except hagfish), ATO, and the IOC taxonomy of living birds. Synonyms from ITIS and Catalog of Life were attached if the primary name matched a name in the existing taxonomy. Subspecies names were added to their parent species as synonyms (not subclasses). The taxonomy is currently in the OBO format used for TTO and ATO, which includes the use of the Taxonomic Rank Vocabulary to tag taxa with specified rank.

Other Taxonomic Resources

Amniotes

• Birds The IOC checklist provides a current taxonomy and common names, but no taxonomic synonyms.
• Mammals Wilson and Reader (1993) is the standard, but the available electronic version of their taxonomy is IP encumbered.

Taxonomic (hierarchy) Resources

• NCBI This was used to fill in the gaps (non-avian amniotes) in the current proposed VTO. This provides taxonomy for GenBank submissions (including fossil taxa), but does not claim to be an authoritative source (and generally doesn't cover taxa that have not been submitted). It does provide some taxonomic synonyms as well.
• ITIS Has some vetting by area experts, but coverage is not complete (nor uncontroversial).

Nomenclature Resources

These can provide links to additional synonyms and resources (e.g., TTO uses fishbase to provide common names and links to their pages). Taxonomic synonyms are particularly useful as aids to data curation, but common names can assist users in browsing the website. Some nomenclature resources act as aggregators of names from other sources (e.g., Catalogue of Life incorporates names from ITIS. Taxonomic resources (above) can be used as sources of names as well.

• Fishbase - their taxonomy is close to TTO (both based on Catalog of Fishes), but TTO uses it strictly as a name resource.
• Global Names Index (GNI)
• Catalogue of Life

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)

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.

• 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