Our paper describing the Vertebrate Taxonomy Ontology (VTO) is published! See: http://www.jbiomedsem.com/content/4/1/34 .
One primary objective for Phenoscape and similar projects is to aggregate phenotypic data from multiple studies to named taxa, which in many phylogenetic studies are species but also might be at higher taxonomic levels such as genera or families. While there are many widely used taxonomies that include rich sampling of species and higher taxa, for example Bill Eschmeyer’s widely used Catalog of Fishes, there are few vetted “bridging” taxonomies that allow for aggregating data across, say, fishes, amphibians, and mammals. This problem becomes even more acute when you consider integrating data for extinct taxa as well. As a first step towards addressing this issue for vertebrates, we created the Vertebrate Taxonomy Ontology (VTO) that brings together taxonomies from NCBI, AmphibiaWeb, the Catalog of Fishes (via the previously existing Teleost Taxonomy Ontology), and the Paleobiology Database. The resulting curated taxonomy contains more than 106,000 terms, more than 104,000 additional synonyms, and extensive cross-referencing to these existing taxonomies. The Phenoscape Knowledgebase will leverage this taxonomic ontology by allowing for phenotype statistics to be displayed by taxon, including coarse measures of the extent of annotation coverage and phenotypic variation. Though phenotypes may be annotated to a species, the use of an ontological framework for the taxonomic hierarchy facilitates aggregating phenotypes to higher levels, such as genera or families. In the future, we hope to be able to integrate other excellent and rich sources of taxon-specific taxonomies, such as that in the Reptile Database or the International Ornithologists’ Union Bird List. This is a work-in-progress and the Phenoscape team is certainly interested to integrate new taxonomic sources as well as explore different ways that such a resource can be used and developed by the larger community.
Phenoscape 