title: 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.
  
  
  RESULTS
  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
  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.
authors.affiliation: National Evolutionary Synthesis Center, Durham, North Carolina, United States of America. balhoff@nescent.org
authors.forename: James P
authors.initials: JP
authors.lastname: Balhoff
authors.forename: Wasila M
authors.initials: WM
authors.lastname: Dahdul
authors.forename: Cartik R
authors.initials: CR
authors.lastname: Kothari
authors.forename: Hilmar
authors.initials: H
authors.lastname: Lapp
authors.forename: John G
authors.initials: JG
authors.lastname: Lundberg
authors.forename: Paula
authors.initials: P
authors.lastname: Mabee
authors.forename: Peter E
authors.initials: PE
authors.lastname: Midford
authors.forename: Monte
authors.initials: M
authors.lastname: Westerfield
authors.forename: Todd J
authors.initials: TJ
authors.lastname: Vision
mesh_terms: D044822:Biodiversity; D005075:Biological Evolution; D019295:Computational Biology / Q000379:methods*; D020407:Internet; D010641:Phenotype; D012660:Semantics; D012984:Software
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