PheSom: a term frequency-based method for measuring human phenotype similarity on the basis of MeSH vocabulary

Frontiers in Genetics

Genetics

Ling Gao¹  Xinhua Liu²  Zhonghai Fang³  Ju Wang³  Yonglin Peng⁴ 

[1] School of Basic Medical Sciences, Hangzhou, Zhejiang, China;School of Basic Medical Sciences, Hangzhou, Zhejiang, China;School of Biomedical Engineering and Technology, Tianjin, China;School of Biomedical Engineering and Technology, Tianjin, China;Shanghai Center for Systems Biomedicine, Shanghai, China;

关键词: phenotype;    mesh;    OMIM;    similarity score;    FIDC;   

DOI  :  10.3389/fgene.2023.1185790

 received in 2023-03-14, accepted in 2023-06-21,  发布年份 2023

来源: Frontiers

【 摘 要 】

Background: Phenotype similarity calculation should be used to help improve drug repurposing. In this study, based on the MeSH terms describing the phenotypes deposited in OMIM, we proposed a method, namely, PheSom (Phenotype Similarity On MeSH), to measure the similarity between phenotypes. PheSom counted the number of overlapping MeSH terms between two phenotypes and then took the weight of every MeSH term within each phenotype into account according to the term frequency-inverse document frequency (FIDC). Phenotype-related genes were used for the evaluation of our method.Results: A 7,739 × 7,739 similarity score matrix was finally obtained and the number of phenotype pairs was dramatically decreased with the increase of similarity score. Besides, the overlapping rates of phenotype-related genes were remarkably increased with the increase of similarity score between phenotypes, which supports the reliability of our method.Conclusion: We anticipate our method can be applied to identifying novel therapeutic methods for complex diseases.

【 授权许可】

Unknown   
Copyright © 2023 Liu, Gao, Peng, Fang and Wang.