diego-s/pmcxml

Tools for searching and parsing full text XML articles and tables in Pubmed Central

pmcXML

pmcXML is an R package to download and parse XML documents from Pubmed Central (PMC).

Use devtools to install the package

library(devtools)
install_github("cstubben/pmcXML")

The pmcSupp function also requires a number of Unix dependencies (unzip, unoconv, pdftotext) to read zip, word tables and pdf supplementary files.

Additional details about the package are on the wiki pages and in BMC Bioinformatics.

Stubben, CJ and JC Challacombe, 2014. Mining locus tags in PubMed Central to improve microbial gene annotation. BMC Bioinformatics 15:43.