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J Bioinform Comput Biol. 2015 Dec;13(6):1542002. doi: 10.1142/S0219720015420020. Epub 2015 Sep 9.

MeSHSim: An R/Bioconductor package for measuring semantic similarity over MeSH headings and MEDLINE documents.

Author information

1
* School of Computer Science, Fudan University, Shanghai 200433, P. R. China.
2
† Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, Shanghai 200433, P. R. China.
3
‡ School of Information Management, Wuhan University, Wuhan 430072, P. R. China.
4
§ Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan.

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.

KEYWORDS:

MEDLINE documents; MeSH; R/bioconductor package; semantic similarity

PMID:
26471719
DOI:
10.1142/S0219720015420020
[Indexed for MEDLINE]

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