Abstract
AbstractPhenex is a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic variation using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Despite the centrality of the phenotype to so much of biology, traditions for communicating information about phenotypes are idiosyncratic to different disciplines. Phenotypes seem to elude standardized descriptions due to the variety of traits that compose them and the difficulty of capturing the complex forms and subtle differences among organisms that we can readily observe. Consequently, phenotypes are refractory to attempts at data integration that would allow computational analyses across studies and study systems. Phenex addresses this problem by allowing scientists to employ standard ontologies and syntax to link computable phenotype annotations to evolutionary character matrices, as well as to link taxa and specimens to ontological identifiers. Ontologies have become a foundational technology for establishing shared semantics, and, more generally, for capturing and computing with biological knowledge.
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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