fulltext

Get full text research articles

Checkout the package docs and the fulltext manual to get started.

rOpenSci has a number of R packages to get either full text, metadata, or both from various publishers. The goal of fulltext is to integrate these packages to create a single interface to many data sources.

fulltext makes it easy to do text-mining by supporting the following steps:

Search for articles - ft_search
Fetch articles - ft_get
Get links for full text articles (xml, pdf) - ft_links
Extract text from articles / convert formats - ft_extract
Collect all texts into a data.frame - ft_table

Previously supported use cases, extracted out to other packages:

Collect bits of articles that you actually need - moved to package pubchunks
Supplementary data from papers has been moved to the suppdata package

It’s easy to go from the outputs of ft_get to text-mining packages such as tm and quanteda.

Data sources in fulltext include:

Crossref - via the rcrossref package
Public Library of Science (PLOS) - via the rplos package
Biomed Central
arXiv - via the aRxiv package
bioRxiv - via the biorxivr package
PMC/Pubmed via Entrez - via the rentrez package
Scopus (https://www.scopus.com/) - internal tooling
Semantic Scholar (https://www.semanticscholar.org/) - internal tooling
Many more are supported via the above sources (e.g., Royal Society Open Science is available via Pubmed)
We will add more, as publishers open up, and as we have time…See the master list here

Authentication: A number of publishers require authentication via API key, and some even more draconian authentication processes involving checking IP addresses. We are working on supporting all the various authentication things for different publishers, but of course all the OA content is already easily available. See the Authentication section in ?fulltext-package after loading the package.

We’d love your feedback. Let us know what you think in the issue tracker (https://github.com/ropensci/fulltext/issues)

Article full text formats by publisher: https://docs.ropensci.org/fulltext/articles/formats

Installation

Stable version from CRAN

install.packages("fulltext")

Development version from GitHub

remotes::install_github("ropensci/fulltext")

Load library

library('fulltext')

Interoperability with other packages downstream

Note: this example not included in vignettes as that would require the two below packages in Suggests here. To see many examples and documentation see the package docs and the fulltext manual.

cache_options_set(path = (td <- 'foobar'))
res <- ft_get(c('10.7554/eLife.03032', '10.7554/eLife.32763'), type = "pdf")
library(readtext)
x <- readtext::readtext(file.path(cache_options_get()$path, "*.pdf"))

library(quanteda)
quanteda::corpus(x)

Contributors

Scott Chamberlain https://github.com/sckott
Will Pearse https://github.com/willpearse
Katrin Leinweber https://github.com/katrinleinweber

fulltext

Installation

Interoperability with other packages downstream

Contributors

Meta