Ontologies

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Revision as of 13:54, 26 March 2012 by Peteremidford@yahoo.com (talk | contribs) (→‎Fish Collection Codes Ontology)

Phenoscape has developed several multispecies anatomy ontologies for vertebrates to describe (annotate) variation in phenotypes. These ontologies are publicly available and being used and extended by the community (view the list). Where possible, we are sharing existing ontologies (e.g., PATO) with the broader biological community for the greatest interoperability across data types. These anatomy ontologies reside in the OBO CVS-based version-control system, from which they are regularly loaded into the NCBO BioPortal where they can be readily browsed, searched, and visualized. The ontologies are also available for download as .obo files from the BioPortal or OBO Foundry, and can be viewed using the OBO-Edit desktop software.

Anatomy Ontologies

Phenoscape is coordinating the integration of anatomy ontologies from vertebrate models (zebrafish, Xenopus, mouse) and multi-species lineages (vertebrates, teleost fishes, amphibians, amniotes). The development plan and release schedule for these anatomy ontologies detail the working plan for their integration. We hold regular project anatomy ontology conference calls to discuss development with the curators of these ontologies.

Vertebrate Musculoskeletal Anatomy Ontology (VAO)

VAO contains terms representing structures in the musculoskeletal system of vertebrates. It references terms from the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO) Biological Process, Cell Ontology (CL), and the Phenotype and Trait Ontology (PATO). VAO can be downloaded at the OBO Foundry and browsed at BioPortal.

See the VAO development plan for more details on its release schedule and development.

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

Amniote Anatomy Ontology (AMAO)

AMAO is a new anatomy ontology being developed for amniotes. It will import skeletal terms from VAO and non-skeletal terms from the Uber Anatomy Ontology (Uberon).

See the AMAO development plan for more details on its release schedule and development.

Amphibian Anatomy Ontology (AAO)

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

See the AAO development plan for more details on its release schedule and development.

Mouse Adult Gross Anatomy (MA)

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. Term requests can be submitted on the mouse anatomy tracker

See the MA development plan for more details on its release schedule and development.

Teleost Anatomy Ontology (TAO)

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. Term requests can be submitted to the TAO tracker.

See the TAO development plan for more details on its release schedule and development.

Xenopus Anatomy Ontology (XAO)

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.

See the XAO development plan for more details on its release schedule and development.

Zebrafish Anatomical Ontology (ZFA)

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. Term requests can be submitted to the ZFA tracker.

See the ZFA development plan for more details on its release schedule and development.

Taxonomy Ontologies

Teleost Taxonomy Ontology (TTO)

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 (ATO)

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

Vertebrate Taxonomy Ontology (VTO)

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.

Fossil Taxa

  • Paleobiology Database This covers all groups represented in the fossil record - we have implemented a way to incorporate bulk taxonomy downloads in the VTO. We are still somewhat uncertain about how hierarchies are (dynamically) built in this resource.

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).
  • Catalogue of Life Claimed to incorporate all of ITIS plus Species2000. Updated quarterly.

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. 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) - Extensive list of names but no hierarchy.

Additional documentation

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. The TAXRANK vocabulary can be browsed at Bioportal.

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 master list, from which the OBO ontology is generated is available as a [ https://docs.google.com/spreadsheet/ccc?key=0AmUeHhtnDeCZcDZpa1YwVG82Zlhwcmc4OTk4elJhTlE google docs spreadsheet]. 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

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.

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