Anatomy Ontology Development Plan

The Phenoscape project is coordinating the development and integration of multispecies and single species ontologies for teleosts, zebrafish, amphibians, frog, 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

See ontology release schedule for detailed implementation schedule.

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 ontologies. These shared terms will be obsoleted from and subsequently 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). 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 should be used). However, because MODs currently cannot import terms, shared terms will instead be duplicated in single species ontologies and cross-reference to the term in the external ontology added. For example, because XAO and AAO both contain the term ‘radio-ulna’, the term XAO:radio-ulna will cross-reference the ID for AAO: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.
• Terms from external ontologies (GO, PATO, Cell) will be cross-referenced

Zebrafish Anatomical Ontology(ZFA)

ZFA will add cross references to VAO terms. Cross references to TAO will be also be updated as needed.

Teleost Anatomy Ontology (TAO)

TAO will import VAO terms. Any TAO terms applicable outside of Teleostei will be obsoleted and added to VAO for subsequent import.

Xenopus Anatomy Ontology (XAO)

XAO will add cross references to VAO terms.

Amphibian Anatomy Ontology (AAO)

AAO will import VAO terms in Year 2. Any AAO terms applicable outside of Amphibia will be obsoleted and added to VAO for subsequent import.

Next target release date: July 2011

• Terms currently under “unclassified anatomical entity” will be given is_a parents

Mouse Adult Gross Anatomy (MA)

MA will add cross references to VAO terms.

Amniote Anatomy Ontology (AMAO)

AMAO will import skeletal terms from VAO and non-skeletal terms from Uberon.

Initial release date: Late August 2011

• VAO terms will be imported