Anatomy Ontology Development Plan

The Phenoscape project is coordinating the development and integration of multispecies and single species ontologies for teleosts, zebrafish, amphibians, Xenopus, amniotes, and mouse. The focus of ontology development in year 1 is the limb/fin skeletal branch.

The development of these ontologies follows OBO Foundry principles. Importing ontology terms is the preferred mechanism for using shared terms and VAO will be imported into TAO, AAO, and AMAO. However, 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 terms, we will be exploring importing terms from external ontologies. In the interim, the existing MOD vertebrate ontologies will duplicate shared terms with cross-references to equivalent terms in external ontologies.

Year 1 Development Plan

Vertebrate Anatomy Ontology (VAO)

VAO will be expanded to include terms in the muscular and skeletal systems that are shared by two or more multispecies vertebrate ontologies. These shared terms will be imported into the multispecies ontologies. For example, ‘femur’, a term applicable to AAO and AMAO, will be added to VAO and imported into AMAO (Year 1) and AAO (Year 2). Shared terms that already exist in multispecies ontologies will be obsoleted, given a "replaced_by" relationship to the relevant VAO term, and the shared term subsequently imported into the ontology. Terms shared by a multispecies ontology and its corresponding single-species ontology (e.g., AAO and XAO) would also ideally be imported from the multispecies ontology into the single species ontology (or rather, a single ontology for that taxonomic group could be used). However, because MODs currently cannot import terms, shared terms will instead be duplicated in single species ontologies and cross-referenced to the term in the external ontology. For example, because XAO and AAO both contain ‘radio-ulna’, the term XAO term will cross-reference the AAO ID for radio-ulna.

Next target release date: Late August 2011

Features:

• 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 in Boulder, CO (June 1-3, 2011)
• Relationships to terms from external ontologies (GO, PATO, CL) will be included

Teleost Anatomy Ontology (TAO)

Next target release date: Late August 2011

Features:

• VAO musculo-skeletal terms will be imported, and existing TAO terms applicable outside of Teleostei will be obsoleted and added to VAO for subsequent import

Amphibian Anatomy Ontology (AAO)

Next target release date: Late August 2011

Features:

• children of "unclassified anatomical entity" will be given appropriate is_a parents

As a long term goal, AAO and XAO will be aligned, XAO terms will cross reference their AAO parents, and these ontologies will be regularly synchronized. However, because AAO development is not scheduled for the first year, AAO will be merged into XAO and development of AAO frozen until year 2. Specifically, AAO terms applicable to Xenopus will be given two IDs in XAO (an XAO ID and AAO alt-ID), and those not applicable to Xenopus will be given a single ID (the AAO ID with new XAO prefix). In year 2, AAO will be cloned from XAO and AAO development restarted for curation of amphibian publications. XAO will retain xrefs to Xenopus-applicable AAO terms and will obsolete AAO terms not aplicable to Xenopus. The two ontologies will be synchronized regularly. AAO will import VAO terms, and any AAO terms applicable outside of Amphibia will be obsoleted and added to VAO for subsequent import.

Amniote Anatomy Ontology (AMAO)

Next target release date:

Features:

• In the initial release, musculo-skeletal terms from VAO and non-skeletal terms from the amniote subset of the Uber Anatomy Ontology (Uberon) will be imported into AMAO

Zebrafish Anatomical Ontology (ZFA)

ZFA terms are cross referenced to TAO terms, and these cross references will be maintained and updated as needed. In addition, cross references to VAO musculo-skeletal terms will be added.

Next target release date:

Features:

Xenopus Anatomy Ontology (XAO)

(see desciption of XAO/AAO merge above)

Next target release date:

Features:

• AAO terms will be merged with XAO terms
• Cross references to VAO musculo-skeletal terms will be added

Mouse Adult Gross Anatomy (MA)

Next target release date:

Features:

• Cross references to VAO musculo-skeletal terms will be added