Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

Haendel, Melissa A.; Balhoff, James P.; Bastian, Frederic B.; Blackburn, David C.; Blake, Judith A.; Bradford, Yvonne; Comte, Aurelie; Dahdul, Wasila M.; Dececchi, Thomas A.; Druzinsky, Robert E.; Hayamizu, Terry F.; Ibrahim, Nizar; Lewis, Suzanna E.; Mabee, Paula M.; Niknejad, Anne; Robinson-Rechavi, Marc; Sereno, Paul C.; Mungall, Christopher J.

doi:10.1186/2041-1480-5-21

Title: Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

Journal Article · Wed Jan 01 00:00:00 EST 2014 · Journal of Biomedical Semantics

DOI:https://doi.org/10.1186/2041-1480-5-21· OSTI ID:1626677

Haendel, Melissa A. ^[1]; Balhoff, James P. ^[2]; Bastian, Frederic B. ^[3]; Blackburn, David C. ^[4]; Blake, Judith A. ^[5]; Bradford, Yvonne ^[6]; Comte, Aurelie ^[3]; Dahdul, Wasila M. ^[7]; Dececchi, Thomas A. ^[8]; Druzinsky, Robert E. ^[9]; Hayamizu, Terry F. ^[5]; Ibrahim, Nizar ^[10]; Lewis, Suzanna E. ^[11]; Mabee, Paula M. ^[8]; Niknejad, Anne ^[3]; Robinson-Rechavi, Marc ^[3]; Sereno, Paul C. ^[10]; Mungall, Christopher J. ^[11]

Oregon Health and Science Univ., Portland, OR (United States). Dept. of Medical Informatics and Epidemiology
Univ. of North Carolina, Chapel Hill, NC (United States). Dept. of Biology; National Evolutionary Synthesis Center, Durham, NC (United States)
Univ. of Lausanne (Switzerland). Dept. of Ecology and Evolution; Swiss Inst. of Bioformatics, Lausanne (Switzerland)
California Academy of Sciences, San Francisco, CA (United States). Dept. of Vertebrate Zoology and Anthropology
The Jackson Lab., Bar Harbor, ME (United States)
Univ. of Oregon, Eugene, OR (United States). The Zebrafish Model Organism Database
National Evolutionary Synthesis Center, Durham, NC (United States); Univ. of South Dakota, Vermillion, SD (United States). Dept. of Biology
Univ. of South Dakota, Vermillion, SD (United States). Dept. of Biology
Univ. of Chicago, IL (United States). Dept. of Oral Biology
Univ. of Chicago, IL (United States). Dept. of Organismal Biology and Anatomy
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Background: Elucidating 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. Results: Previously, 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. Conclusions: The 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/

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1626677

Journal Information:: Journal of Biomedical Semantics, Vol. 5, Issue 1; ISSN 2041-1480

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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