title: MeSHSim: An R/Bioconductor package for measuring semantic similarity over MeSH headings and MEDLINE documents.
abstract: Currently, all MEDLINE documents are indexed by medical subject headings (MeSH). Computing semantic similarity between two MeSH headings as well as two documents has become very important for many biomedical text mining applications. We develop an R package, MeSHSim, which can compute nine similarity measures between MeSH nodes, by which similarity between MeSH headings as well as MEDLINE documents can be easily computed. Also, MeSHSim supports querying hierarchy information of a MeSH heading and retrieving MeSH headings of a query document, and can be easily integrated into pipelines for any biomedical text analysis tasks. MeSHSim is released under general public license (GPL), and available through Bioconductor and from Github at https://github.com/JingZhou2015/MeSHSim.
authors.affiliation: * School of Computer Science, Fudan University, Shanghai 200433, P. R. China.|† Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, Shanghai 200433, P. R. China.
authors.forename: Jing
authors.initials: J
authors.lastname: Zhou
authors.affiliation: * School of Computer Science, Fudan University, Shanghai 200433, P. R. China.|† Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, Shanghai 200433, P. R. China.
authors.forename: Yuxuan
authors.initials: Y
authors.lastname: Shui
authors.affiliation: * School of Computer Science, Fudan University, Shanghai 200433, P. R. China.|† Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, Shanghai 200433, P. R. China.
authors.forename: Shengwen
authors.initials: S
authors.lastname: Peng
authors.affiliation: ‡ School of Information Management, Wuhan University, Wuhan 430072, P. R. China.
authors.forename: Xuhui
authors.initials: X
authors.lastname: Li
authors.affiliation: § Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Mamitsuka
authors.affiliation: * School of Computer Science, Fudan University, Shanghai 200433, P. R. China.|† Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, Shanghai 200433, P. R. China.
authors.forename: Shanfeng
authors.initials: S
authors.lastname: Zhu
mesh_terms: D000465:Algorithms; D057225:Data Mining / Q000379:methods*; D016239:MEDLINE; D046650:Medical Subject Headings
keywords: MEDLINE documents; MeSH; R/bioconductor package; semantic similarity