Uberon: towards a comprehensive multi-species anatomy ontology

The lack of a single unified species-neutral ontology covering the anatomy of a variety of metazoans is a hindrance to translating model organism research to human health. We have developed an Uber-anatomy ontology to fill this need, filling the gap between the CARO upper-level ontology and species-specific anatomical ontologies. Introduction A number of anatomical ontologies (AOs) exist for specific organisms such as human, mouse and fish, many of which utilize the Common Anatomy Reference Ontology (CARO)1 to structure the highest-level nodes. However, there is as yet a lack of a unified species-neutral ontology containing representations of embryonic and mature anatomical entities that conforms to OBO Foundry principles, similar to the Gene Ontology (GO) for gene function. Other cross species terminologies exist, such as MeSH, Gemina Anatomy and the Minimum Anatomy Terminology, but these resources are not formal ontologies, utilizing a single relation, and therefore do not provide an adequate substrate for reasoning across species. Results Uberon is a preliminary multi-species metazoan anatomy ontology created primarily to fulfil two requirements: (1) support translational research by allowing comparison of phenotypes across species and (2) provide logical cross-product definitions for GO biological process terms. The first version of Uberon was generated automatically by aligning existing species-specific anatomy ontologies (ssAOs) and anatomical reference ontologies, and then partially manually curated. Uberon retains reverse is_a links to the ssAOs, such that these can be used in cross-species inferencing and queries. A term is generally included in Uberon if it is a generalization over two or more existing species-specific anatomy terms. For example, UBERON:dorsal_root_ganglion subsumes ZFA:dorsal_root_ganglion, MA:dorsal_root_ganglion, and others. Uberon is homology-independent, and thus contains general terms for analogous structures that have evolved multiple times, such as eye. Future versions of Uberon may include evolutionary relationships between structures, along the lines of the TAO and BILA ontologies. Uberon attempts to employ is_a, part_of, overlaps, and developmental relations in the same manner as ssAOs. The current version of the ontology has 2808 terms, and 5110 links between terms, and 9339 links out to other AOs (Table 1), 1643 Wikipedia cross-references, and has been referenced in 682 GO cross-products. Ontology Type Xrefs FMA Adult human 2302 MA Adult mouse 1495 EHDAA Embryonic human 838