School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China.
Department of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, 518055, China.
BMC Genomics. 2018 Aug 13;19(Suppl 6):571. doi: 10.1186/s12864-018-4927-z.
The Human Phenotype Ontology (HPO) is one of the most popular bioinformatics resources. Recently, HPO-based phenotype semantic similarity has been effectively applied to model patient phenotype data. However, the existing tools are revised based on the Gene Ontology (GO)-based term similarity. The design of the models are not optimized for the unique features of HPO. In addition, existing tools only allow HPO terms as input and only provide pure text-based outputs.
We present PhenoSimWeb, a web application that allows researchers to measure HPO-based phenotype semantic similarities using four approaches borrowed from GO-based similarity measurements. Besides, we provide a approach considering the unique properties of HPO. And, PhenoSimWeb allows text that describes phenotypes as input, since clinical phenotype data is always in text. PhenoSimWeb also provides a graphic visualization interface to visualize the resulting phenotype network.
PhenoSimWeb is an easy-to-use and functional online application. Researchers can use it to calculate phenotype similarity conveniently, predict phenotype associated genes or diseases, and visualize the network of phenotype interactions. PhenoSimWeb is available at http://120.77.47.2:8080.
人类表型本体（HPO）是最受欢迎的生物信息学资源之一。最近，基于 HPO 的表型语义相似性已被有效地应用于模拟患者表型数据。然而，现有的工具是基于基于基因本体（GO）的术语相似性进行修订的。这些模型的设计没有针对 HPO 的独特特征进行优化。此外，现有的工具仅允许 HPO 术语作为输入，并且仅提供纯基于文本的输出。
我们提出了 PhenoSimWeb，这是一个 Web 应用程序，允许研究人员使用从基于 GO 的相似性度量中借鉴的四种方法来衡量基于 HPO 的表型语义相似性。此外，我们还提供了一种考虑 HPO 独特属性的方法。并且，PhenoSimWeb 允许输入描述表型的文本，因为临床表型数据始终以文本形式存在。PhenoSimWeb 还提供了一个图形可视化界面，用于可视化生成的表型网络。
PhenoSimWeb 是一个易于使用且功能齐全的在线应用程序。研究人员可以方便地使用它来计算表型相似性，预测与表型相关的基因或疾病，并可视化表型相互作用的网络。PhenoSimWeb 可在 http://120.77.47.2:8080 访问。
