Jan 252014

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.


Filed under: Taxonomy Ontology, Vertebrates
Mar 072012

On 15–16 February 2012, I visited NESCent to work with Peter Midford, Jim Balhoff, and, especially, Wasila Dahdul. The focus of my trip was to push forward on the continued development of the Amphibian Anatomical Ontology and the integration of phenotypic data for amphibians into the larger Phenoscape project.

With Peter Midford, I worked to make a significant update to the Amphibian Taxonomy Ontology based largely on a recent revision to the higher-level taxonomy used on AmphibiaWeb (for which I am part of the steering committee). AmphibiaWeb provides an excellent resource for Phenoscape and other related projects because it provides a list of currently recognized species of living amphibians and is updated daily.

The majority of my visit was spent working with Wasila Dahdul on issues related to the Amphibian Anatomy Ontology (AAO) and on curating our first evolutionary dataset related to the fin–limb transition (Ruta et al., 2003). During this work, we plowed through a significant portion of AAO terms lacking parent terms (either adding parents or synonymizing the terms with others in either VAO or AAO). We also evaluated whether to add terms to the AAO that are present in the Xenopus Anatomy Ontology (XAO; Xenopus is a genus of African frogs used as a model system) but absent in the AAO. In some cases, this led to recommending that those terms be removed from the XAO. As we have started to curate morphological characters related to the limbs from the study by Ruta et al. (2003), we encountered many terms not present in existing anatomy ontologies, such as AAO or the Vertebrate Anatomy Ontology. Some terms had been slated for inclusion in the Amniote Anatomy Ontology (AmAO) being developed by Nizar Ibrahim and Paul Sereno (University of Chicago). Because these terms are also present in non-amniotes, we are recommending that they be migrated from the AmAO to the higher-level VAO.

As we start to focus on curating phenotypes from the literature of vertebrate paleontology, a few issues are emerging. One important issue is that curation of data from paleontological studies will likely necessitate adding a field to our information for specimens to accommodate free text alongside museum abbreviations and catalog numbers. The reason for this is that paleontological studies can rely on a combination of materials, including both specimens and examination of literature. We will also need to add to and refine the collection of museum codes used to curate specimen data. These last points about accurately curating data related to specimens examined are important if we are to use the Phenoscape knowledgebase to point to records for those same specimens in on-line databases, or if databases (such as those for museum collections) want to point to records of specimens in the Phenoscape knowledgebase.

Filed under: Anatomy Ontology, Data Curation, Ontology, Training, Vertebrates