title: Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution.
abstract: The abundance of phenotypic diversity among species can enrich our knowledge of development and genetics beyond the limits of variation that can be observed in model organisms. The Phenoscape Knowledgebase (KB) is designed to enable exploration and discovery of phenotypic variation among species. Because phenotypes in the KB are annotated using standard ontologies, evolutionary phenotypes can be compared with phenotypes from genetic perturbations in model organisms. To illustrate the power of this approach, we review the use of the KB to find taxa showing evolutionary variation similar to that of a query gene. Matches are made between the full set of phenotypes described for a gene and an evolutionary profile, the latter of which is defined as the set of phenotypes that are variable among the daughters of any node on the taxonomic tree. Phenoscape's semantic similarity interface allows the user to assess the statistical significance of each match and flags matches that may only result from differences in annotation coverage between genetic and evolutionary studies. Tools such as this will help meet the challenge of relating the growing volume of genetic knowledge in model organisms to the diversity of phenotypes in nature. The Phenoscape KB is available at http://kb.phenoscape.org.
authors.affiliation: Department of Biology, University of North Carolina, Chapel Hill, North Carolina.|US National Evolutionary Synthesis Center, Durham, North Carolina.
authors.forename: Prashanti
authors.initials: P
authors.lastname: Manda
authors.affiliation: Department of Biology, University of North Carolina, Chapel Hill, North Carolina.|US National Evolutionary Synthesis Center, Durham, North Carolina.
authors.forename: James P
authors.initials: JP
authors.lastname: Balhoff
authors.affiliation: US National Evolutionary Synthesis Center, Durham, North Carolina.|Center for Genomic and Computational Biology, Duke University, Durham, North Carolina.
authors.forename: Hilmar
authors.initials: H
authors.lastname: Lapp
authors.affiliation: Department of Biology, University of South Dakota, Vermillion, South Dakota.
authors.forename: Paula
authors.initials: P
authors.lastname: Mabee
authors.affiliation: Department of Biology, University of North Carolina, Chapel Hill, North Carolina.|US National Evolutionary Synthesis Center, Durham, North Carolina.
authors.forename: Todd J
authors.identifier: http://orcid.org/0000-0002-6133-2581
authors.initials: TJ
authors.lastname: Vision
mesh_terms: D000818:Animals; D005075:Biological Evolution; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D056726:Genetic Association Studies / Q000379:methods*; D006801:Humans; D051188:Knowledge Bases; D010641:Phenotype
keywords: candidate genes; phenotypic variation; semantic similarity