Abstract
BackgroundPhenotypic 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 FindingsHere 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/SignificanceAnnotation 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.
Highlights
The manifestation of evolution at the organismal level is the phenotype, the set of observable traits inhering in an individual organism as a result of the interaction of heredity, environmental influences, and developmental processes
The unfolding of the phenotype from a fertilized egg is at the core of developmental biology, the inference of gene function through the phenotypic effect of allelic differences is a major focus of genetics, and using phenotypes to inform and interpret phylogenies in living and fossil organisms is at the core of systematics and comparative biology
One of the most common and most formalized approaches within evolutionary biology is in the field of phylogenetic systematics, where the variable organismal features and their variants in different taxa are itemized and given numeric codes in a character-by-taxon matrix
Summary
The manifestation of evolution at the organismal level is the phenotype, the set of observable traits inhering in an individual organism as a result of the interaction of heredity, environmental influences, and developmental processes. Phenotypes are refractory to attempts at data integration that would allow computational analyses across studies and study systems [1] We address this problem at its root by development of a configurable software tool that employs standard ontologies and syntax to create computable phenotype annotations. One of the most common and most formalized approaches within evolutionary biology is in the field of phylogenetic systematics, where the variable organismal features (characters) and their variants in different taxa (character states) are itemized and given numeric codes in a character-by-taxon matrix. Neither NEXUS, nor several other standards that have been developed for descriptive species data [12,13], has built-in support for linking ontology terms to the text strings used to describe characters, character states, and taxonomic names. A companion paper describes the standards that have been developed within the Phenoscape project for the curation process [17]
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