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，能够突破模式生物观测变异的局限，拓展我们在发育生物学与遗传学领域的认知边界。表型图谱知识库（Phenoscape Knowledgebase，KB）旨在支持对物种间表型变异的探索与发掘。由于该知识库中的表型均通过标准本体进行注释，因此可将演化表型与模式生物中遗传扰动产生的表型进行对比分析。为展示该方法的应用效能，本文综述了如何利用该知识库检索演化变异与查询基因相似的类群。匹配过程基于基因的完整表型描述集与演化特征谱完成，后者被定义为分类树任意节点的子分支类群间存在变异的表型集合。表型图谱的语义相似性界面允许用户评估每一组匹配结果的统计学显著性，并标记出仅由遗传研究与演化研究间注释覆盖范围差异所导致的匹配结果。此类工具将助力解决将模式生物中日益增长的遗传学知识，与自然中丰富的表型多样性建立关联的核心挑战。表型图谱知识库可通过以下网址访问：http://kb.phenoscape.org。