Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon
Year: 2014
Type: article
Abstract: 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/
Source: Journal of Biomedical Semantics
Authors: Melissa A Haendel, James P Balhoff, Frederic B Bastian, David C Blackburn, Judith A Blake, Yvonne Bradford, Aurelie Comte, Wasila M Dahdul, Thomas A Dececchi, Robert E Druzinsky, Terry F Hayamizu, Nizar Ibrahim, Suzanna E Lewis, Paula M Mabee, Anne Niknejad, Marc Robinson-Rechavi, Paul C Sereno, Christopher J Mungall
Institutions: Oregon Health & Science University, University of North Carolina at Chapel Hill, National Evolutionary Synthesis Center, SIB Swiss Institute of Bioinformatics, University of Lausanne, California Academy of Sciences, Jackson Laboratory, University of Oregon, University of South Dakota, University of Illinois Chicago, University of Chicago, Lawrence Berkeley National Laboratory
Language: English
Subfield: Health Informatics
Field: Medicine
Domain: Health Sciences
Open Access status: gold
Estimated APC paid: $1,590
Funders: National Science Foundation, U.S. Department of Energy, National Evolutionary Synthesis Center, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, National Institutes of Health, Office of Science, National Human Genome Research Institute, Division of Emerging Frontiers, Basic Energy Sciences
Awards: COLLABORATIVE RESEARCH: ABI Innovation: A novel database and ontology for evolutionary analyses of mammalian feeding physiology, G1286236842, G1286251239, G1414775356, G1445641779, G1478932903, Gene Ontology Consortium, G1816284028, G1863003419, G20317863, Bioinformatic study of molecular evolution in the context of animal development and anatomy, G2391278426, G2517729222, G2610688614, G2618837358, G2843378090, ZFIN: The Zebrafish Model Organism Database, G30714459, G3083819904, Linking Evolution to Genomics Using Phenotype Ontologies, G3621937125, G3652311727, G365575497, G3712952848, The Monarch Initiative: Linking Diseases to Model Organism Resources, G382641700, G419881185, G42916606, G4501827968, ZFIN: The Zebrafish Model Organism Database, G498139845, COLLABORATIVE RESEARCH: ABI Development: Ontology-enabled reasoning across phenotypes from evolution and model organisms, G544591541, Collaborative research: ABI Development: Ontology-enabled reasoning across phenotypes from evolution and model organisms, G5849692847, RCN: Phenotype Ontology Research Coordination Network, G650090426, G6652958823, CSBE: A Place for Evolutionary Synthesis in North Carolina's Research Triangle, G747304092, National Evolutionary Synthesis Center, G805243471, G969889393
OpenAlex ID: W2143742443