The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes
Midford, P.E.; Dececchi, T.; Balhoff, J.P.; Dahdul, W.M.; Ibrahim, N.; Lapp, H.; Lundberg, J.G.; Mabee, P.M.; Sereno, P.C.; Westerfield, M.; Vision, T.J.; Blackburn, D.C. (2013). The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes. Journal of Biomedical Semantics 4(1): 34. https://dx.doi.org/10.1186/2041-1480-4-34
In: Journal of Biomedical Semantics. BIOMED CENTRAL LTD: London. e-ISSN 2041-1480, more
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| Author keywords |
Data integration, Evolutionary biology, Paleontology, Taxonomic rank |
| Authors | | Top |
- Midford, P.E.
- Dececchi, T.
- Balhoff, J.P.
- Dahdul, W.M.
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- Ibrahim, N.
- Lapp, H.
- Lundberg, J.G.
- Mabee, P.M.
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- Sereno, P.C.
- Westerfield, M.
- Vision, T.J.
- Blackburn, D.C.
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| Abstract |
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. 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. 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. |
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