Phenex: ontological annotation of phenotypic diversity.
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 articlePermalink
https://hdl.handle.net/10161/10192Published Version (Please cite this version)
10.1371/journal.pone.0010500Publication 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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Show full item recordScholars@Duke
Hilmar Lapp
Dir, IT

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