Mining data from PLOS and PubMed Central (PMC) | Authorea

lterrat's bookmarks 2017-02-19


"This post was inspired from Jon Tennant's post on his blog (here). He was talking about the number of papers on paleontology field published in PLOSone. His post was mainly based on his code using `rplos` package (Github repo/CRAN repo) from `ropensci` community. Jon's post was kind of fire up my R life again, especially in the field of text mining. So in this post, I will connect this original post with my research about analyzing biodiversity of Cikapundung riverbank area (here/Figshare).  

This post is going to tap paper data from PLOS and PubMed Central (PMC) using R, RStudio, rplos package, and rplotly package. So how it goes:
  • First you need to install R then R Studio (not the other way around),
  • Fire up R Studio,
  • Install and load the library rplos and rplotly,
  • PLOS data: tap PLOS data directly and plot the result,
  • PMC data: they don't have any package for direct tapping (yet), but here's the workaround explained from several sources. You have to go Flink system to do some queries based on key words. Be sure to choose you database by pulling down the menu,
  • Export the query result,
  • Then do some analysis and plotting from R Studio. 
Then I write some code following Jon's code from his blog and add it with some my own."


From feeds:

Open Access Tracking Project (OATP) » lterrat's bookmarks

Tags: oa.mining oa.pubmed_central oa.plos_one oa.code4oa

Date tagged:

02/19/2017, 20:36

Date published:

02/19/2017, 15:36