Journal article
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.
- Haendel MA Department of Medical Informatics & Epidemiology, Oregon Health & Science University, Portland, OR, USA.
- Balhoff JP Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA ; National Evolutionary Synthesis Center, Durham, NC, USA.
- Bastian FB Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Blackburn DC Department of Vertebrate Zoology and Anthropology, California Academy of Sciences, San Francisco, CA 94118, USA.
- Blake JA The Jackson Laboratory, Bar Harbor, ME 04609, USA.
- Bradford Y The Zebrafish Model Organism Database, University of Oregon, Eugene, OR 97403, USA.
- Comte A Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Dahdul WM National Evolutionary Synthesis Center, Durham, NC, USA ; Department of Biology, University of South Dakota, Vermillion, SD 57069, USA.
- Dececchi TA Department of Biology, University of South Dakota, Vermillion, SD 57069, USA.
- Druzinsky RE Department of Oral Biology, University of Illinois-Chicago, Chicago, IL 60612, USA.
- Hayamizu TF The Jackson Laboratory, Bar Harbor, ME 04609, USA.
- Ibrahim N Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA.
- Lewis SE Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA.
- Mabee PM Department of Biology, University of South Dakota, Vermillion, SD 57069, USA.
- Niknejad A Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Robinson-Rechavi M Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Sereno PC Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA.
- Mungall CJ Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA.
- 2014-07-11
Published in:
- Journal of biomedical semantics. - 2014
English
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/
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/
- Language
-
- English
- Open access status
- gold
- Identifiers
-
- DOI 10.1186/2041-1480-5-21
- PMID 25009735
- Persistent URL
- https://folia.unifr.ch/global/documents/259271
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