Ontologies

The Phenoscape project is coordinating the development and integration of multispecies and single species anatomy ontologies for vertebrates, with taxonomic focus on teleosts, zebrafish, amphibians, Xenopus, amniotes, and mouse. These ontologies are publicly available and being used and extended by the community (view the list). Where possible, we are also reusing external ontologies (e.g., PATO) from the broader biological community for the greatest interoperability across data types. The development of these ontologies follows OBO Foundry principles as much as possible, including reuse of ontology terms (by import or MIREOT) as the preferred mechanism for using shared terms. These anatomy ontologies are available from 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 OBO Foundry and can also be viewed using the OBO-Edit or Protege desktop software.

The existing model organism databases are largely hardcoded to reference identifiers for their own ontologies (e.g., MGI database reads MA term identifiers). In the long term, we will be exploring how to import terms into these ontologies. In the interim, the existing MOD vertebrate ontologies will continue to link to external terms using a cross-referencing strategy to external ontology identifiers (see Interontology links)

Anatomy Ontologies

Ontology coordination

• New personnel training topics for building and using ontologies
• Ontology editing workflow
• See also the course materials for the anatomy ontology course held at NESCent in August of 2012

In the past we have held regular project anatomy ontology conference calls to discuss development with the curators of the various anatomy ontologies listed below. The limb/fin branch was the focus of ontology development in year 1. Currently, we coordinate our development calls with the Phenotype RCN vertebrate working group monthly calls. Information about these calls is sent to the obo-anatomy, phenotype-rcn vertebrate google groups, and the phenoscape project listservs. These calls are open to everyone and call in info and notes from them is available at the Vertebrate Working Group Wiki Page.

In addition, the Phenoscape curators have been meeting weekly to have joint ontology editing sessions. Please let us know if you would like to join us, Melissa Haendel has been coordinating these sessions (haendel@ohsu.edu).

Phenoscape-ext

Phenoscape-ext contains the TAO, AAO, and VSAO combined with Uberon. This adds an additional 2500+ classes to the core Uberon, all contributed by the Phenoscape project. Phenoscape-ext is our first foray into working directly in OWL.

• Ontology update requests can be made on the Uberon term request tracker: [1]
• Source edit file available here: [2]
• Release files are available here:

http://purl.obolibrary.org/obo/uberon/ext.obo

http://purl.obolibrary.org/obo/uberon/ext.owl

phenoscape-ext.owl will remain the editors version. The release uberon/ext.owl retains the import chains and is pre-reasoned. uberon/ext.obo merges the import chain into one ontology because obo does not have good support for imports. Mant of the other uberon derived artefacts such as composite-metazoan do not use ext but this may be changed in the future. See uberon.org for details of all the various cuts.

We will continue to reconcile the issues that arose during this merge (started in August, 2012, first release on Feb 22, 2013), so you may continue to see some issues. This ontology will be used by Phenoscape for annotation of evolutionary characters.

• Further information about Uberon and the Phenoscape-ext merge

Vertebrate Skeletal Anatomy Ontology (VSAO)

VSAO contains terms representing structures in the skeletal 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). VSAO can be downloaded at the OBO Foundry and browsed at BioPortal. Development of the VSAO is described in Dahdul et al. (2012)

• Release version available here: [3]

Note that VSAO as released represents the outcome of the skeletal anatomy workshop held at NESCent and corresponding paper in PLOS ONE. Note also that VSAO development moving forward has been merged into the Phenoscape-ext ontology described above.

New skeletal terms for the limb/fin and cranial skeleton have and will continue to be added to the Phenoscape-ext ontology based on work done at the Phenotype RCN Vertebrate Working Group meeting in Boulder, CO (June 1-3, 2011) and from ongoing work.

Amphibian Anatomy Ontology (AAO)

AAO is a multispecies ontology for amphibian anatomy.

• Download AAO from the OBO Foundry and browse at BioPortal
• Source edit directory available here. The current version (April 2012) includes terms merged from the Xenopus Anatomy Ontology and updates from David Blackburn and Wasila Dahdul.

NOTE: as per above case with VSAO, AAO has been merged into phenoscape-ext and is no longer under 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.
• Further documentation about TAO

NOTE: as per above case with VSAO, the TAO has been merged into phenoscape-ext and is no longer under development.

Mouse Adult Gross Anatomy (MA)

The Adult Mouse Anatomy (MA) ontology contains terms that represent structures in the postnatal mouse (Mus) and is used to annotate gene expression and phenotypes for the mouse at Mouse Genome Informatics (MGI) and other resources. Development of the MA is described in Hayamizu et al. (2005).

• The MA is available for download at the OBO Foundry and can be browsed using the Mouse Anatomy Browser.
• Term requests can be submitted on the mouse anatomy tracker

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.
• Term tracker is available here: [4]
• Source directory is available here: [5]

Zebrafish Anatomical Ontology (ZFA)

ZFA is used by ZFIN to annotate mutant phenotypes for the model organsim zebrafish (Danio rerio).

• Download from the OBO Foundry or browse at the BioPortal.
• Term requests can be submitted to the ZFA tracker.
• Edit version is kept internally at ZFIN, but a prerelease edit version is available at [6]

ZFA terms are cross referenced to TAO terms, and these cross references will be maintained and updated as needed.

Taxonomy Ontologies

Vertebrate Taxonomy Ontology (VTO)

The Vertebrate Taxonomy Ontology (Midford, Dececchi, et al. 2013) includes the TTO, ATO, and uses the NCBI taxonomy as a source covering amniotes and basal chordates outside the scope of the TTO. The ontology has an assigned OBO purl http://purl.obolibrary.org, and there is a repository at https://code.google.com/p/vertebrate-taxonomy-ontology/. The current release covers vertebrates and was built by starting with the NCBI taxonomy for vertebrates and splicing in TTO (except hagfish), and the downloadable amphibiaweb taxonomy.  Subspecies names were added to their parent species as synonyms (not subclasses). The taxonomy is currently in the available in OWL format, as generated by the OBO release tool. It also uses the Taxonomic Rank Vocabulary to tag taxa with specified rank.

• NCBI This taxonomy provides the amniote portions of the current 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.
• 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.

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). TTO (hence VTO) uses it as a source of common names and includes links to Fishbase's species pages.
• Global Names Index (GNI) - Extensive list of names.

Teleost Taxonomy Ontology (TTO)

The Teleost Taxonomy Ontology (TTO) is derived from the Catalog of Fishes (see also the representation on BioPortal, which can be navigated on-line). The TTO was developed from the Phenoscape I project and provides coverage of fish in the VTO. The TTO is updated in concert with Catalog of Fishes updates.

• The TTO in OWL format is available here.
• Browse TTO at BioPortal

Amphibian Taxonomy Ontology (ATO)

The ATO has been deprecated in favor of generating the Amphibian component of the VTO directly from Amphibiaweb.

• The version available at BioPortal is very old and neither used in VTO nor recommended.

Taxonomic Rank Vocabulary (TAXRANK)

During 2010, we released a separate Taxonomic Rank Vocabulary, 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 is available in OWL format here.
• The vocabulary can be browsed at Bioportal.

Fish Collection Codes Vocabulary

There is a flat 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-format ontology is generated is available as a 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

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)

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 (PATO)
• Evidence Code Ontology
• OBO-relations
• Spatial Ontology
• Comparative Data Analysis Ontology (CDAO), developed by the EvoInfo working group at NESCent, and used within the Phenoscape OBD data repository.