{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,5]],"date-time":"2026-07-05T05:01:16Z","timestamp":1783227676727,"version":"3.54.6"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2023,5,29]],"date-time":"2023-05-29T00:00:00Z","timestamp":1685318400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62272105"],"award-info":[{"award-number":["62272105"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Municipal Science and Technology Major Project","award":["2018SHZDZX01"],"award-info":[{"award-number":["2018SHZDZX01"]}]},{"name":"ZJ Lab"},{"DOI":"10.13039\/501100013314","name":"111 Project","doi-asserted-by":"publisher","award":["B18015"],"award-info":[{"award-number":["B18015"]}],"id":[{"id":"10.13039\/501100013314","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Research Center for Brain Science and Brain-Inspired Intelligence Technology"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Human Phenotype Ontology (HPO)-based approaches have gained popularity in recent times as a tool for genomic diagnostics of rare diseases. However, these approaches do not make full use of the available information on disease and patient phenotypes. We present a new method called Phen2Disease, which utilizes the bidirectional maximum matching semantic similarity between two phenotype sets of patients and diseases to prioritize diseases and genes. Our comprehensive experiments have been conducted on six real data cohorts with 2051 cases (Cohort 1, n\u2009=\u2009384; Cohort 2, n\u2009=\u2009281; Cohort 3, n\u2009=\u2009185; Cohort 4, n\u2009=\u2009784; Cohort 5, n\u2009=\u2009208; and Cohort 6, n\u2009=\u2009209) and two simulated data cohorts with 1000 cases. The results of the experiments showed that Phen2Disease outperforms the three state-of-the-art methods when only phenotype information and HPO knowledge base are used, particularly in cohorts with fewer average numbers of HPO terms. We also observed that patients with higher information content scores have more specific information, leading to more accurate predictions. Moreover, Phen2Disease provides high interpretability with ranked diseases and patient HPO terms presented. Our method provides a novel approach to utilizing phenotype data for genomic diagnostics of rare diseases, with potential for clinical impact. Phen2Disease is freely available on GitHub at https:\/\/github.com\/ZhuLab-Fudan\/Phen2Disease.<\/jats:p>","DOI":"10.1093\/bib\/bbad172","type":"journal-article","created":{"date-parts":[[2023,5,30]],"date-time":"2023-05-30T06:05:53Z","timestamp":1685426753000},"source":"Crossref","is-referenced-by-count":18,"title":["Phen2Disease: a phenotype-driven model for disease and gene prioritization by bidirectional maximum matching semantic similarities"],"prefix":"10.1093","volume":"24","author":[{"given":"Weiqi","family":"Zhai","sequence":"first","affiliation":[{"name":"Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University , Shanghai 200433 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaodi","family":"Huang","sequence":"additional","affiliation":[{"name":"School of Computing , Mathematics, and Engineering, , Albury, NSW 2640 , Australia"},{"name":"Charles Sturt University , Mathematics, and Engineering, , Albury, NSW 2640 , Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nan","family":"Shen","sequence":"additional","affiliation":[{"name":"Department of Infectious Disease , Shanghai Children's Medical Center, National Children\u2019s Medical Center, School of Medicine, , Shanghai, 200127 , China"},{"name":"Shanghai Jiao Tong University , Shanghai Children's Medical Center, National Children\u2019s Medical Center, School of Medicine, , Shanghai, 200127 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shanfeng","family":"Zhu","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University , Shanghai 200433 , China"},{"name":"Shanghai Qi Zhi Institute , Shanghai 200030 , China"},{"name":"Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education , Shanghai 200433 , China"},{"name":"Shanghai Key Laboratory of Intelligent Information Processing and Shanghai Institute of Artificial Intelligence Algorithm, Fudan University , Shanghai 200433 , China"},{"name":"Zhangjiang Fudan International Innovation Center , Shanghai 200433 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,5,29]]},"reference":[{"issue":"7","key":"2023072020021728100_ref1","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1038\/gim.2015.148","article-title":"Clinical application of whole-exome sequencing across clinical indications","volume":"18","author":"Retterer","year":"2016","journal-title":"Genet Med"},{"issue":"7","key":"2023072020021728100_ref2","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1038\/ng.3304","article-title":"Factors influencing success of clinical genome sequencing across a broad spectrum of 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