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Phenex: ontological annotation of phenotypic diversity.

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Date
2010-05-05
Authors
Balhoff, James P
Dahdul, Wasila M
Kothari, Cartik R
Lapp, Hilmar
Lundberg, John G
Mabee, Paula
Midford, Peter E
Westerfield, Monte
Vision, Todd J
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Abstract
BACKGROUND: Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge. METHODOLOGY/PRINCIPAL FINDINGS: Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices. CONCLUSIONS/SIGNIFICANCE: Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.
Type
Journal article
Subject
Biodiversity
Biological Evolution
Computational Biology
Internet
Phenotype
Semantics
Software
Permalink
https://hdl.handle.net/10161/10192
Published Version (Please cite this version)
10.1371/journal.pone.0010500
Publication Info
Balhoff, James P; Dahdul, Wasila M; Kothari, Cartik R; Lapp, Hilmar; Lundberg, John G; Mabee, Paula; ... Vision, Todd J (2010). Phenex: ontological annotation of phenotypic diversity. PLoS One, 5(5). pp. e10500. 10.1371/journal.pone.0010500. Retrieved from https://hdl.handle.net/10161/10192.
This is constructed from limited available data and may be imprecise. To cite this article, please review & use the official citation provided by the journal.
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Lapp

Hilmar Lapp

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