Pubmed Central web scraper quick start

Cathy Yeh

Scrape articles on Pubmed Central (PMC) for figures, e.g. plots of tumor growth inhibition for a particular drug, and store scraped results in a SQLite database.

Query the database for a particular drug and plot-type to generate html reports displaying links to the source articles, along with article abstracts, captured figures, and captions.

Depends on R Packages

  • RSQLite
  • DBI
  • RCurl
  • XML
  • httr
  • rvest
  • stringr
  • knitr

First time using scraper: create a SQLite database

createSQLiteDatabase.R creates a SQLite database with the schema below that is used to store the scraped results

table: article

pmcid | doi | title | journal | year | authors | abstract | keywords

table: figure

topic | plot_type | img_url | pmcid

table: figure_text

img_url | fig_name | caption

Scripts to scrape PMC and generate html reports

pubmedcentral_scraper.R calls on

  • eSearch.R
  • eFetch.R
  • scrapeArticle.R
  • myDb.sqlite (created by createSQLiteDatabase.R)

markdown_and_plot.R calls on

  • generate_markdown_code.R
  • myDb.sqlite

Running the webscraper

set scraper settings in pubmedcentral_scraper.R

## <---------USER INPUT STARTS HERE---------> = "myDb.sqlite"
retmax = 10
query.topic = c("Docetaxel", "Docetaxol")
topic = "Docetaxel"
query.plottype = c("tumor growth", "tumor volume",
                   "tumor size", "tumor inhibition",
                   "tumor growth inhibition", "tgi",
                   "tumor response", "tumor regression")
plot_type = "TGI"

## <---------USER INPUT ENDS HERE----------->

Run the scraper:


Visualize web scraping results

edit top of markdown_and_plot.R

## <---------USER INPUT STARTS HERE--------->

## name of database where scraper results are stored
db = "myDb.sqlite"

## topic/drug label for database
topic = "Docetaxel"

## plot type label for database
plot_type = "TGI"

## filename of generated markdown code
rmd.filename = "makeHTMLplots.rmd"

## <---------USER INPUT ENDS HERE----------->

generate html report for scraper results


Excerpt of sample report

topic: “Docetaxel”; plot_type: “TGI”