Difference between revisions of "Anatomy Ontology Development Plan"
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| − | The Phenoscape project is coordinating the integration and development of multispecies | + | The Phenoscape project is coordinating the integration and development of multispecies and single species vertebrate 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. | 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. | ||
Revision as of 16:17, 30 June 2011
The Phenoscape project is coordinating the integration and development of multispecies and single species vertebrate 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.
Contents
Year 1 Development Plan
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). However, terms shared by a multispecies ontology and its corresponding single-species ontology (e.g., AAO and XAO) will not be added to VAO. These terms should 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, single species ontologies will instead duplicate shared terms and cross-reference the external ontology. For example, because XAO and AAO both contain the term ‘radio-ulna’, XAO will cross-reference the AAO ID for this term.
Implementation of taxonomic constraints in VAO
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)
Will add VAO xrefs; will update term relationships
Teleost (TAO)
TAO will import only teleost applicable VAO terms. For example, ‘femur’ would not be imported. Will import teleost subset of VAO.
