pubchunks

Get chunks of XML articles

Package API

• pub_tabularize
• pubguesspublisher
• 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

r install.packages("pubchunks")

Development version from GitHub

r remotes::install_github("ropensci/pubchunks")

Load library

r library('pubchunks')

Working with files

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

```r pub_chunks(x, "abstract")

>

> 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")

>

> 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")

>

> 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"))

>

> 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): Watson G.N.. 1949. Teoriia besselevykh funktsii. N

```

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

```r xml <- paste0(readLines(x), collapse = "") pub_chunks(xml, "title")

>

> 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

```r xml <- paste0(readLines(x), collapse = "") xml <- xml2::readxml(xml) pubchunks(xml, "title")

>

> 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()

r install.packages("fulltext")

```r library("fulltext") x <- fulltext::ftget('10.1371/journal.pone.0086169') pubchunks(fulltext::ft_collect(x), sections="authors")

> $plos

> $plos$10.1371/journal.pone.0086169

>

> 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

```r x <- system.file("examples/elife1.xml", package = "pubchunks") res <- pubchunks(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

```r library(rcrossref) library(dplyr)

res <- crworks(filter = list( fulltexttype = "application/xml", licenseurl="http://creativecommons.org/licenses/by/4.0/")) links <- bindrows(res$data$link) %>% filter(content.type == "application/xml") download.file(links$URL[1], (i <- tempfile(fileext = ".xml"))) pubchunks(i)

>

> 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)

>

> from: file

> publisher/journal: hindawi/BioMed Research International

> sections: all

> showing up to first 5:

> front (n=2): nested list

> body (n=49): Oxidative stress and Reactive Oxygen Species (ROS)

> back (n=4): nested list

> title (n=1): Selected Enzyme Inhibitory Effects of Euphorbia ch ...

> doi (n=1): 10.1155/2018/1219367

download.file(links$URL[20], (k <- tempfile(fileext = ".xml"))) pub_chunks(k)

>

> from: file

> publisher/journal: hindawi/Case Reports in Pathology

> sections: all

> showing up to first 5:

> front (n=2): nested list

> body (n=16): Bonnetti et al. first noted in 1992 an unusual cel

> back (n=3): nested list

> title (n=1): An Inguinal Perivascular Epithelioid Cell Tumor Me ...

> doi (n=1): 10.1155/2018/5749421

```

Meta

• Please report any issues or bugs.
• License: MIT
• Get citation information for pubchunks: citation(package = 'pubchunks')
• Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.