Abstract
BackgroundElucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent ‘natural’ phenotypic variation across species. Our aim has been to integrate ssAOs and msAOs for various purposes, including establishing links between phenotypic variation and candidate genes.ResultsPreviously, msAOs contained a mixture of unique and overlapping content. This hampered integration and coordination due to the need to maintain cross-references or inter-ontology equivalence axioms to the ssAOs, or to perform large-scale obsolescence and modular import. Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups. As a consequence, independent development of TAO, VSAO, AAO, and vHOG has been discontinued.ConclusionsThe newly broadened Uberon ontology is a unified cross-taxon resource for metazoans (animals) that has been substantially expanded to include a broad diversity of vertebrate anatomical structures, permitting reasoning across anatomical variation in extinct and extant taxa. Uberon is a core resource that supports single- and cross-species queries for candidate genes using annotations for phenotypes from the systematics, biodiversity, medical, and model organism communities, while also providing entities for logical definitions in the Cell and Gene Ontologies.The ontology release files associated with the ontology merge described in this manuscript are available at: http://purl.obolibrary.org/obo/uberon/releases/2013-02-21/Current ontology release files are available always available at: http://purl.obolibrary.org/obo/uberon/releases/
Highlights
Elucidating disease and developmental dysfunction requires understanding variation in phenotype
A major goal for the Model Organism Database (MOD) is to query across anatomical phenotype data to support the identification of relevant genes linked to human diseases
Classes from any source ontology that were not represented in Uberon were placed in an OWL-formatted extension ontology, which imports the core Uberon and extends classes in the core
Summary
Elucidating disease and developmental dysfunction requires understanding variation in phenotype. To standardize the upper-level terms (for example, “tissue” and “acellular structure”) across different ssAOs, the Common Anatomy Reference Ontology (CARO) was developed [9] This did not resolve all these issues, as CARO was not designed to provide a large set of terms for specific structures shared across species, but rather to provide an organizational framework for constructing anatomy ontologies. A major goal for the MODs is to query across anatomical phenotype data to support the identification of relevant genes linked to human diseases (see [10]) To facilitate this goal, we constructed the Über Anatomy Ontology (Uberon), a metazoan multi-species anatomy ontology, to provide a generalization of anatomical structures across the MODs [11]. To compare ‘natural’ phenotypic variation across species, a number of efforts have been made to build taxon-specific multispecies AOs (msAOs)
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