Using meshes for MeSH term enrichment and semantic analyses

Guangchuang Yu

doi:10.1093/bioinformatics/bty410

Using meshes for MeSH term enrichment and semantic analyses

Bioinformatics. 2018 Nov 1;34(21):3766-3767. doi: 10.1093/bioinformatics/bty410.

Author

Guangchuang Yu^{1

2}

Affiliations

¹ Institute of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
² State Key Laboratory of Emerging Infectious Disease, School of Public Health, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China.

PMID: 29790928
DOI: 10.1093/bioinformatics/bty410

Abstract

Summary: Medical Subject Headings (MeSH) is the NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH provides unique and comprehensive annotations for life science. The meshes package implements measurement of the semantic similarity of MeSH terms and gene products to help using MeSH vocabulary in knowledge mining. Enrichment analysis to extract the biological meanings from gene list, expression profile and genomic regions is also provided using MeSH annotation. Meshes supports more than 70 species and provides high quality visualization methods to help interpreting analysis results.

Availability and implementation: meshes is released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (https://www.bioconductor.org/packages/meshes).

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

Computational Biology
Genomics*
MEDLINE*
Medical Subject Headings*
PubMed
Semantics*
Software*