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 or MIREOTing 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 and a move toward importing terms from external ontologies will take time to implement. Because of this, some of the existing MOD vertebrate ontologies will instead 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 skeletal terms 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.

Implementation of taxonomic constraints in VAO

necessary? Taxonomically constrained subsets of VAO will be generated so that the terms imported into a subontology include only those designated as applicable to the taxonomic group of interest (e.g., TAO would import VAO using the "teleost" subset). This can be accomplished by using either taxonomically-defined subsets or never_in_taxon/only_in_taxon links to generate taxonomic slims of VAO.

Zebrafish (ZFA)

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

Teleost (TAO)

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

Xenopus (XAO)

XAO will add cross references to VAO terms.

Amphibian (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.

Mouse Adult Gross Anatomy (MA)

MA will add cross references to VAO terms.

Amniote Anatomy Ontology (AMAO)

AMAO will import VAO terms.