Jul 212014
 

Over the years, a number of different vertebrate anatomy ontologies have been developed. Some of these are dedicated to a single model species, or to human. Others have been developed to describe phenotypic variation across species, and these cover a broad range of species. In particular:

This lead to considerable duplication of effort, as common anatomical
structures such as ‘pectoral girdle‘ were represented in all five ontologies
(as well as their single species counterparts):

Haendel et al fig 1

Pectoral girdle and related concepts in Uberon, with cross-references to other ontologies shown (Fig 1, Haendel et al)

It was difficult for the Phenoscape group to integrate data across all these ontologies, as this required that curators kept mutual cross-references up to date, a time-consuming and error-prone task.

As a result, the maintainers of these ontologies agreed to join forces and build a common ontology.This work is described in a new paper in the ontologies special issue of the Journal of Biomedical Semantics:

Haendel MA, Balhoff JP, Bastian FB et al  Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon Journal of Biomedical Semantics 2014, 5:21  doi:10.1186/2041-1480-5-21

The group selected Uberon as the core ontology, as it had the broadest coverage, was already well-integrated with the single-species ontologies, and was adapted for OWL reasoning. The curators of these ontologies worked long and hard to integrate their work, with input from anatomy experts and developers of single-species ontologies, revealing many interesting differences in the way structures are represented across species along the way. For example, the representation of teeth in the combined ontology had to be flexible enough to accommodate teeth that are in widely variable locations and configurations:

Figure 4. Diversity of tooth locations

The number of classes merged is shown in figure 2 of the paper:

Figure 2. Overlap and contributions from source ontologies. A) Venn diagram showing the extent of cross-referenced content between msAOs prior to the merge.. B) Ontology evolution and integration into Uberon

 

As a result of this effort, we have a common anatomy ontology with broad and deep coverage for vertebrate anatomy. For a variety of viewing options, see the Uberon website. For examples of use for data integration see:

Like most ontologies, work is ongoing and we are constantly striving to improve depth, coverage and quality. We’re currently actively improving the representation of facial muscles in the ontology based on the FEED ontology. We are also working on a federated approach for bringing in invertebrate anatomy ontologies, many of which are developed under the auspices of the Phenotype RCN  including the Arthropod Anatomy Ontology, the Poriferan anatomy ontology [Thacker et al, accepted, JBMS], the cephalopod  ontology and the ctenophore ontology. We welcome feedback from everyone!

Mar 012012
 

On the last day of a very successful Phenotype RCN meeting at Nescent last week , we held an impromptu session on OBO to OWL mappings.  This was based on the a recent workshop run for GO curators by myself (David Osumi-Sutherland), Chris Mungall,  Simon Jupp and Jane Lomax.  By popular demand, I’ve posted my slides on slideshare.

The original workshop also included an intro to Protégé 4 by Simon Jupp [warning: word doc] as well as a set of problem solving exercises consisting of a set of folders each featuring one or more test ontologies and a README with instructions. For best results, you should checkout the whole repository of exercises using an svn client: svn checkout http://oboformat.googlecode.com/svn/docs/tutorial/ obo2owl_tut_read_only
Details of the software required for these exercises can be found at http://tinyurl.com/86w9xud