In ropensci/bmc: Search the BiomedCentral API and get full text articles.

bmc

library("knitr")
hook_output <- knitr::knit_hooks$get("output")
knitr::knit_hooks$set(output = function(x, options) {
   lines <- options$output.lines
   if (is.null(lines)) {
     return(hook_output(x, options))  # pass to default hook
   }
   x <- unlist(strsplit(x, "\n"))
   more <- "..."
   if (length(lines)==1) {        # first n lines
     if (length(x) > lines) {
       # truncate the output, but add ....
       x <- c(head(x, lines), more)
     }
   } else {
     x <- c(if (abs(lines[1])>1) more else NULL, 
            x[lines], 
            if (length(x)>lines[abs(length(lines))]) more else NULL
           )
   }
   # paste these lines together
   x <- paste(c(x, ""), collapse = "\n")
   hook_output(x, options)
 })

knitr::opts_chunk$set(
  comment = "#>",
  collapse = TRUE,
  warning = FALSE, 
  message = FALSE
)

An R interface to BMC search API and full text XML

API DOCS: http://www.biomedcentral.com/about/api

No API key is required to use the BMC API.

Package Status and Installation

Installation instructions

Development Version

install.packages("devtools")
devtools::install_github("ropensci/bmc")

Usage

library("bmc")

Search

out <- bmc_search(terms = 'fire', limit=2)
out@results$entries[[1]]

The object returned from bmc_search is an object of class bmc. The default print gives back a list of length N, where each element has the contents for the article in question. We can inspect further elements of the bmc object with the @ symbol. We can get the urls element...

out@urls

...which has the urls you can use to go the paper in a browser

browseURL(out@urls[1])

which opens the paper in your default browser

We can also inspect the ids element, which has a list equal to the number you requested, where each element is of length 2, with a arxId, and a url. These two are used to construct the download url if you use bmc_xml.

out@ids

Get full text XML

You can either pass in a url to the uris parameter in the bmc_xml function, or pass in the output of the bmc_search function to bmc_xml using the first parameter obj. First, passing in a url:

uri <- 'http://www.biomedcentral.com/content/download/xml/1471-2393-14-71.xml'
bmc_xml(uris=uri)

Now the output from bmc_search()

out <- bmc_search(terms = 'science', limit=5)
dat <- bmc_xml(out)
length(dat)

Inspect the xml

dat[[1]]

Parse and search XML

Once you have XML content, you can go to work with e.g., xpath.

uri <- 'http://www.biomedcentral.com/content/download/xml/1471-2393-14-71.xml'
xml <- bmc_xml(uris=uri)
library("XML")
xpathApply(xml[[1]], "//abs", xmlValue)