The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes
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Midford, Peter E, et al. The Vertebrate Taxonomy Ontology: a Framework for Reasoning Across Model Organism and Species Phenotypes. BioMed Central Ltd, 2013. https://doi.org/10.17615/dynz-8121APA
Midford, P., Dececchi, T., Balhoff, J., Dahdul, W., Ibrahim, N., Lapp, H., Lundberg, J., Mabee, P., Sereno, P., Westerfield, M., Vision, T., & Blackburn, D. (2013). The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes. BioMed Central Ltd. https://doi.org/10.17615/dynz-8121Chicago
Midford, Peter E, Thomas Dececchi, James P Balhoff, Wasila M Dahdul, Nizar Ibrahim, Hilmar Lapp, John G Lundberg et al. 2013. The Vertebrate Taxonomy Ontology: a Framework for Reasoning across Model Organism and Species Phenotypes. BioMed Central Ltd. https://doi.org/10.17615/dynz-8121- Creator
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Midford, Peter E
- Other Affiliation: Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA; National Evolutionary Synthesis Center, Durham, North Carolina, USA
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Dececchi, Thomas
- Other Affiliation: Department of Biology, University of South Dakota, Vermillion, South Dakota, USA
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Balhoff, James P
- Affiliation: College of Arts and Sciences, Department of Biology
- Other Affiliation: National Evolutionary Synthesis Center, Durham, North Carolina, USA
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Dahdul, Wasila M
- Other Affiliation: National Evolutionary Synthesis Center, Durham, North Carolina, USA; Department of Biology, University of South Dakota, Vermillion, South Dakota, USA
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Ibrahim, Nizar
- Other Affiliation: Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA
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Lapp, Hilmar
- Other Affiliation: National Evolutionary Synthesis Center, Durham, North Carolina, USA
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Lundberg, John G
- Other Affiliation: Academy of Natural Sciences, Philadelphia, Pennsylvania, USA
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Mabee, Paula M
- Other Affiliation: Department of Biology, University of South Dakota, Vermillion, South Dakota, USA
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Sereno, Paul C
- Other Affiliation: Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA
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Westerfield, Monte
- Other Affiliation: Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
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Vision, Todd
- Affiliation: College of Arts and Sciences, Department of Biology
- Other Affiliation: National Evolutionary Synthesis Center, Durham, North Carolina, USA
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Blackburn, David C
- Other Affiliation: Department of Vertebrate Zoology and Anthropology, California Academy of Sciences, San Francisco, California, USA
- Abstract
- Abstract Background A hierarchical taxonomy of organisms is a prerequisite for semantic integration of biodiversity data. Ideally, there would be a single, expansive, authoritative taxonomy that includes extinct and extant taxa, information on synonyms and common names, and monophyletic supraspecific taxa that reflect our current understanding of phylogenetic relationships. Description As a step towards development of such a resource, and to enable large-scale integration of phenotypic data across vertebrates, we created the Vertebrate Taxonomy Ontology (VTO), a semantically defined taxonomic resource derived from the integration of existing taxonomic compilations, and freely distributed under a Creative Commons Zero (CC0) public domain waiver. The VTO includes both extant and extinct vertebrates and currently contains 106,947 taxonomic terms, 22 taxonomic ranks, 104,736 synonyms, and 162,400 cross-references to other taxonomic resources. Key challenges in constructing the VTO included (1) extracting and merging names, synonyms, and identifiers from heterogeneous sources; (2) structuring hierarchies of terms based on evolutionary relationships and the principle of monophyly; and (3) automating this process as much as possible to accommodate updates in source taxonomies. Conclusions The VTO is the primary source of taxonomic information used by the Phenoscape Knowledgebase (http://phenoscape.org/), which integrates genetic and evolutionary phenotype data across both model and non-model vertebrates. The VTO is useful for inferring phenotypic changes on the vertebrate tree of life, which enables queries for candidate genes for various episodes in vertebrate evolution.
- Date of publication
- November 22, 2013
- DOI
- Identifier
- Resource type
- Article
- Rights statement
- In Copyright
- Rights holder
- Peter E Midford et al.; licensee BioMed Central Ltd.
- License
- Journal title
- Journal of Biomedical Semantics
- Journal volume
- 4
- Journal issue
- 1
- Page start
- 34
- Language
- English
- Is the article or chapter peer-reviewed?
- Yes
- ISSN
- 2041-1480
- Bibliographic citation
- Journal of Biomedical Semantics. 2013 Nov 22;4(1):34
- Publisher
- BioMed Central Ltd
- Access right
- Open Access
- Date uploaded
- November 29, 2013
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