Data from: Using the Phenoscape Knowledgebase to relate genetic perturbations to phenotypic evolution

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.物种间丰富的表型多样性（phenotypic diversity）能够突破模式生物（model organisms）中可观测的变异范围，拓展我们对发育生物学与遗传学的认知边界。表型图谱知识库（Phenoscape Knowledgebase，KB）旨在支持对物种间表型多样性的探索与发现工作。由于该知识库中的表型均通过标准本体（standard ontologies）进行注释，因此可将演化表型与模式生物中遗传扰动（genetic perturbations）所对应的表型进行比对分析。为展示该方法的应用潜力，本文综述了如何利用该知识库检索与查询基因（query gene）具有相似演化变异的分类群（taxa）。比对将针对基因的全套描述表型与演化特征谱（evolutionary profile）展开，其中演化特征谱被定义为分类树（taxonomic tree）中任意节点的子代类群间存在变异的表型集合。表型图谱知识库的语义相似性检索界面（semantic similarity interface）支持用户对每一组比对结果进行统计学显著性（statistical significance）评估，并标记出仅可能由遗传研究与演化研究间注释覆盖度（annotation coverage）差异导致的比对结果。此类工具将有助于应对一项核心挑战：如何将模式生物中日益增长的遗传学知识，与自然界中丰富的表型多样性建立关联。表型图谱知识库的访问地址为：http://kb.phenoscape.org。