The rich phenotypic diversity that characterizes the vertebrate skeleton results from evolutionary changes in regulation of genes that drive development. Although relatively little is known about the genes that underlie the skeletal variation among fish species, significant knowledge of genetics and development is available for zebrafish. Because developmental processes are highly conserved, this knowledge can be leveraged for understanding the evolution of skeletal diversity. We developed the Phenoscape Knowledgebase (KB; http://kb.phenoscape.org) to yield testable hypotheses of candidate genes involved in skeletal evolution. We developed a community anatomy ontology for fishes and ontology-based methods to represent complex free-text character descriptions of species in a computable format. With these tools, we populated the KB with comparative morphological data from the literature on over 2500 teleost fishes (mainly Ostariophysi) resulting in over 500,000 taxon phenotype annotations. The KB integrates these data with similarly structured phenotype data from zebrafish genes (http://zfin.org). Using ontology-based reasoning, candidate genes can be inferred for the phenotypes that vary across taxa, thereby uniting genetic and phenotypic data to formulate evo-devo hypotheses. The morphological data in the KB can be browsed, sorted, and aggregated in ways that provide unprecedented possibilities for data mining and discovery.

中文翻译：

---

500,000 种鱼类表型：脊椎动物骨骼进化和发育生物学的新信息学景观

脊椎动物骨骼特征丰富的表型多样性是驱动发育的基因调控的进化变化的结果。尽管人们对鱼类骨骼变异背后的基因知之甚少，但斑马鱼的遗传学和发育方面的知识却非常丰富。由于发育过程高度保守，因此可以利用这些知识来理解骨骼多样性的进化。我们开发了 Phenoscape 知识库（KB；http://kb.phenoscape.org），以产生参与骨骼进化的候选基因的可检验假设。我们开发了鱼类的群落解剖学本体和基于本体的方法，以可计算的格式表示物种的复杂自由文本字符描述。借助这些工具，我们在知识库中填充了来自 2500 多种硬骨鱼类（主要是 Ostariophy）文献中的比较形态学数据，从而产生了超过 500,000 个分类单元表型注释。知识库将这些数据与来自斑马鱼基因的类似结构的表型数据整合在一起 (http://zfin.org)。使用基于本体的推理，可以推断出不同类群中不同表型的候选基因，从而将遗传和表型数据结合起来制定进化-发展假说。知识库中的形态数据可以以多种方式浏览、排序和聚合，为数据挖掘和发现提供前所未有的可能性。