Fetch Sections of XML Scholarly Articles

Get chunks of XML scholarly articles without having to know how to work with XML. Custom mappers for each publisher and for each article section pull out the information you want. Works with outputs from package 'fulltext', 'xml2' package documents, and file paths to XML documents.

pubchunks

Get chunks of XML articles

Package API

pub_tabularize
pub_guess_publisher
pub_sections
pub_chunks
pub_providers

The main workhorse function is pub_chunks(). It allows you to pull out sections of articles from many different publishers (see next section below) WITHOUT having to know how to parse/navigate XML. XML has a steep learning curve, and can require quite a bit of Googling to sort out how to get to different parts of an XML document.

The other main function is pub_tabularize() - which takes the output of pub_chunks() and coerces into a data.frame for easier downstream processing.

Supported publishers/sources

eLife
PLOS
Entrez/Pubmed
Elsevier
Hindawi
Pensoft
PeerJ
Copernicus
Frontiers
F1000 Research

If you know of other publishers or sources that provide XML let us know by opening an issue.

We'll continue adding additional publishers.

Installation

Stable version

install.packages("pubchunks")

Development version from GitHub

remotes::install_github("ropensci/pubchunks")

Load library

library('pubchunks')

Working with files

x <- system.file("examples/10_1016_0021_8928_59_90156_x.xml", 
  package = "pubchunks")

pub_chunks(x, "abstract")
#> <pub chunks>
#>   from: file
#>   publisher/journal: elsevier/Journal of Applied Mathematics and Mechanics
#>   sections: abstract
#>   showing up to first 5: 
#>    abstract (n=1): Abstract
#>                
#>                   This pa ...
pub_chunks(x, "title")
#> <pub chunks>
#>   from: file
#>   publisher/journal: elsevier/Journal of Applied Mathematics and Mechanics
#>   sections: title
#>   showing up to first 5: 
#>    title (n=1): On the driving of a piston with a rigid collar int ...
pub_chunks(x, "authors")
#> <pub chunks>
#>   from: file
#>   publisher/journal: elsevier/Journal of Applied Mathematics and Mechanics
#>   sections: authors
#>   showing up to first 5: 
#>    authors (n=1): Chetaev, D.N
pub_chunks(x, c("title", "refs"))
#> <pub chunks>
#>   from: file
#>   publisher/journal: elsevier/Journal of Applied Mathematics and Mechanics
#>   sections: title, refs
#>   showing up to first 5: 
#>    title (n=1): On the driving of a piston with a rigid collar int ...
#>    refs (n=6): 1.G.N.WatsonTeoriia besselevykh funktsiiTheory of

The output of pub_chunks() is a list with an S3 class pub_chunks to make internal work in the package easier. You can easily see the list structure by using unclass().

Working with the xml already in a string

xml <- paste0(readLines(x), collapse = "")
pub_chunks(xml, "title")
#> <pub chunks>
#>   from: character
#>   publisher/journal: elsevier/Journal of Applied Mathematics and Mechanics
#>   sections: title
#>   showing up to first 5: 
#>    title (n=1): On the driving of a piston with a rigid collar int ...

Working with xml2 class object

xml <- paste0(readLines(x), collapse = "")
xml <- xml2::read_xml(xml)
pub_chunks(xml, "title")
#> <pub chunks>
#>   from: xml_document
#>   publisher/journal: elsevier/Journal of Applied Mathematics and Mechanics
#>   sections: title
#>   showing up to first 5: 
#>    title (n=1): On the driving of a piston with a rigid collar int ...

Working with output of fulltext::ft_get()

install.packages("fulltext")

library("fulltext")
x <- fulltext::ft_get('10.1371/journal.pone.0086169', from='plos')
pub_chunks(fulltext::ft_collect(x), sections="authors")
#> $plos
#> $plos$`10.1371/journal.pone.0086169`
#> <pub chunks>
#>   from: xml_document
#>   publisher/journal: plos/PLoS ONE
#>   sections: authors
#>   showing up to first 5: 
#>    authors (n=4): nested list
#> 
#> 
#> attr(,"ft_data")
#> [1] TRUE

Coerce pub_chunks output into data.frame's

x <- system.file("examples/elife_1.xml", package = "pubchunks")
res <- pub_chunks(x, c("doi", "title", "keywords"))
pub_tabularize(res)
#>                   doi                                          title
#> 1 10.7554/eLife.03032 MicroRNA-mediated repression of nonsense mRNAs
#> 2 10.7554/eLife.03032 MicroRNA-mediated repression of nonsense mRNAs
#> 3 10.7554/eLife.03032 MicroRNA-mediated repression of nonsense mRNAs
#> 4 10.7554/eLife.03032 MicroRNA-mediated repression of nonsense mRNAs
#> 5 10.7554/eLife.03032 MicroRNA-mediated repression of nonsense mRNAs
#> 6 10.7554/eLife.03032 MicroRNA-mediated repression of nonsense mRNAs
#>                       keywords .publisher
#> 1                     microRNA      elife
#> 2            nonsense mutation      elife
#> 3 nonsense-mediated mRNA decay      elife
#> 4                          APC      elife
#> 5             intron retention      elife
#> 6  premature termination codon      elife

Get a random XML article

library(rcrossref)
library(dplyr)

res <- cr_works(filter = list(
    full_text_type = "application/xml", 
    license_url="http://creativecommons.org/licenses/by/4.0/"))
links <- bind_rows(res$data$link) %>% filter(content.type == "application/xml")
download.file(links$URL[1], (i <- tempfile(fileext = ".xml")))
pub_chunks(i)
#> <pub chunks>
#>   from: file
#>   publisher/journal: unknown/NA
#>   sections: all
#>   showing up to first 5: 
#>    front (n=0): 
#>    body (n=0): 
#>    back (n=0): 
#>    title (n=0): 
#>    doi (n=0):
download.file(links$URL[13], (j <- tempfile(fileext = ".xml")))
pub_chunks(j)
#> <pub chunks>
#>   from: file
#>   publisher/journal: scientific_research_publishing/Journal of Electromagnetic Analysis and Applications
#>   sections: all
#>   showing up to first 5: 
#>    front (n=2): nested list
#>    body (n=122): Conventional theoretical physics and its Standard 
#>    back (n=1): nested list
#>    title (n=1): Impacts of Revised Quantum Electrodynamics on Fund ...
#>    doi (n=1): 10.4236/jemaa.2018.105008
download.file(links$URL[20], (k <- tempfile(fileext = ".xml")))
pub_chunks(k)
#> <pub chunks>
#>   from: file
#>   publisher/journal: hindawi/BioMed Research International
#>   sections: all
#>   showing up to first 5: 
#>    front (n=2): nested list
#>    body (n=14): Neospora caninum is an obligate intracellular prot
#>    back (n=5): nested list
#>    title (n=1): First Report of Seroprevalence and Risk Factors of ...
#>    doi (n=1): 10.1155/2018/2098908