pubchunks: extract parts of scholarly XML articles

  Scott Chamberlain OCTOBER 16, 2018

pubchunks is a package grown out of the fulltext package. fulltext provides a single interface to many sources of full text scholarly articles. As part of the user flow in fulltext there is an extraction step where fulltext::chunks() pulls parts of articles out of XML format article files.

As part of making fulltext more maintainable and focused on simply fetching articles, and realizing that pulling out bits of structured XML files is a more general problem, we broke out pubchunks into a separate package. fulltext::ft_chunks() and fulltext::ft_tabularize() will eventually be removed and we’ll point users to pubchunks.

The goal of pubchunks is to fetch sections out of XML format scholarly articles. Users do not need to know about XML and all of its warts. They only need to know where their files or XML strings are and what sections they want of each article. Then the user can combine these sections and do whatever they wish downstream; for example, analysis of the text structure or a meta-analysis combining p-values or other data.

The other major format, and more common format, that articles come in is PDF. However, PDF has no structure other than perhaps separate pages, so it’s not really possible to easily extract specific sections of an article. Some publishers provide absolutely no XML versions (cough, Wiley) while others that do a good job of this are almost entirely paywalled (cough, Elsevier). There are some open access publishers that do provide XML (PLOS, Pensoft, Hindawi) - so you have the best of both worlds with those publishers.

pubchunks is still in early days of development, so we’d love any feedback.

Functions in pubchunks

All exported functions are prefixed with pub to help reduce namespace conflicts.

The two main functions are:

  • pub_chunks(): fetch XML sections
  • pub_tabularize(): coerce output of pub_chunks() into data.frame’s

Other functions that you may run in to:

  • pub_guess_publisher(): guess publisher from XML file or character string
  • pub_sections(): sections pubchunks knows how to handle
  • pub_providers(): providers (i.e., publishers) pubchunks knows how to handle explicitly


How it works

When using pub_chunks() we first figure out what publisher the XML comes from. We do this beacause journals from the same publisher often/usually follow the same format/structure, so we can be relatively confident of rules for pulling out certain sections.

Once we have the publisher, we go through each section of the article the user reqeusts, and use the publisher specific XPATH (an XML query language) that we’ve written to extract that section from the XML.

The ouput is a named list, where names are the sections; and the output is an S3 class with a print method to make it more easily digestable.


Installation

The first version of the package has just hit CRAN, so not all binaries are available as of this date.

install.packages("pubchunks")

You may have to install the dev version

remotes::install_github("ropensci/pubchunks")

After sending to CRAN a few days back I noticed a number of things that needed fixing/improving, so you can also try out those fixes:

remotes::install_github("ropensci/[email protected]_chunks")

Load the package

library(pubchunks)


Pub chunks

pub_chunks accepts a file path, XML as character string, xml_document object, or a list of those three things.

We currently support the following publishers, though not all sections below are allowed in every publisher:

  • elife
  • plos
  • elsevier
  • hindawi
  • pensoft
  • peerj
  • copernicus
  • frontiers
  • f1000research

We currently support the following sections, not all of which are supported, or make sense, for each publisher:

  • front - Publisher, journal and article metadata elements
  • body - Body of the article
  • back - Back of the article, acknowledgments, author contributions, references
  • title - Article title
  • doi - Article DOI
  • categories - Publisher’s categories, if any
  • authors - Authors
  • aff - Affiliation (includes author names)
  • keywords - Keywords
  • abstract - Article abstract
  • executive_summary - Article executive summary
  • refs - References
  • refs_dois - References DOIs - if available
  • publisher - Publisher name
  • journal_meta - Journal metadata
  • article_meta - Article metadata
  • acknowledgments - Acknowledgments
  • permissions - Article permissions
  • history - Dates, recieved, published, accepted, etc.

Get an example XML file from the package

x <- system.file("examples/pensoft_1.xml", package = "pubchunks")

Pass to pub_chunks and state which section(s) you want

pub_chunks(x, sections = "abstract")
#> <pub chunks>
#>   from: character
#>   sections: abstract
#>    abstract (n=1): AbstractNineteen species of seed-beetles belonging ...
pub_chunks(x, sections = "aff")
#> <pub chunks>
#>   from: character
#>   sections: aff
#>    aff (n=7): nested list
pub_chunks(x, sections = "title")
#> <pub chunks>
#>   from: character
#>   sections: title
#>    title (n=1): Contribution to the knowledge of seed-beetles (Col ...
pub_chunks(x, sections = c("abstract", "title", "authors", "refs"))
#> <pub chunks>
#>   from: character
#>   sections: abstract, title, authors, refs
#>    abstract (n=1): AbstractNineteen species of seed-beetles belonging ...
#>    title (n=1): Contribution to the knowledge of seed-beetles (Col ...
#>    authors (n=7): nested list
#>    refs (n=13): AntonKW (2010) Catalogue of Palaearctic Coleoptera

You can also pass in a character string of XML, e.g.,

xml_str <- paste0(readLines(x), collapse = "\n")
class(xml_str)
#> [1] "character"
pub_chunks(xml_str, sections = "title")
#> <pub chunks>
#>   from: character
#>   sections: title
#>    title (n=1): Contribution to the knowledge of seed-beetles (Col ...

Or an xml_document object from xml2::read_xml

xml_doc <- xml2::read_xml(x)
class(xml_doc)
#> [1] "xml_document" "xml_node"
pub_chunks(xml_doc, sections = "title")
#> <pub chunks>
#>   from: xml_document
#>   sections: title
#>    title (n=1): Contribution to the knowledge of seed-beetles (Col ...

Or pass in a list of the above objects, e.g., here a list of file paths

pensoft_xml <- system.file("examples/pensoft_1.xml", package = "pubchunks")
peerj_xml <- system.file("examples/peerj_1.xml", package = "pubchunks")
copernicus_xml <- system.file("examples/copernicus_1.xml", package = "pubchunks")
frontiers_xml <- system.file("examples/frontiers_1.xml", package = "pubchunks")
pub_chunks(
  list(pensoft_xml, peerj_xml, copernicus_xml, frontiers_xml),
  sections = c("abstract", "title", "authors", "refs")
)
#> [[1]]
#> <pub chunks>
#>   from: character
#>   sections: abstract, title, authors, refs
#>    abstract (n=1): AbstractNineteen species of seed-beetles belonging ...
#>    title (n=1): Contribution to the knowledge of seed-beetles (Col ...
#>    authors (n=7): nested list
#>    refs (n=13): AntonKW (2010) Catalogue of Palaearctic Coleoptera
#> 
#> [[2]]
#> <pub chunks>
#>   from: character
#>   sections: abstract, title, authors, refs
#>    abstract (n=1): Climate change is predicted to lead to more extrem ...
#>    title (n=1): Storm effects on intertidal invertebrates: increas ...
#>    authors (n=7): nested list
#>    refs (n=60): Alcántara-Carrió et al. (2017)Alcántara-CarrióJSas
#> 
#> [[3]]
#> <pub chunks>
#>   from: character
#>   sections: abstract, title, authors, refs
#>    abstract (n=1): Soil temperatures at various depths are unique par ...
#>    title (n=1): Quality control of 10-min soil temperatures data a ...
#>    authors (n=3): nested list
#>    refs (n=9): 1Bertrand, C., Gonzalez Sotelino, L., and Journée,
#> 
#> [[4]]
#> <pub chunks>
#>   from: character
#>   sections: abstract, title, authors, refs
#>    abstract (n=1): Our current understanding of Antarctic soils is de ...
#>    title (n=1): Metagenomic Analysis of a Southern Maritime Antarc ...
#>    authors (n=8): nested list
#>    refs (n=56): AislabieJ.BroadyP.SaulD. (2006). Culturable hetero
#> 
#> attr(,"ft_data")
#> [1] FALSE

Last, since we broke pubchunks out of fulltext package we support fulltext here as well.

library("fulltext")
dois <- c('10.1371/journal.pone.0086169', '10.1371/journal.pone.0155491', 
  '10.7554/eLife.03032')
x <- fulltext::ft_get(dois)
pub_chunks(fulltext::ft_collect(x), sections="authors")
#> $plos
#> $plos$`10.1371/journal.pone.0086169`
#> <pub chunks>
#>   from: xml_document
#>   sections: authors
#>    authors (n=4): nested list
#> 
#> $plos$`10.1371/journal.pone.0155491`
#> <pub chunks>
#>   from: xml_document
#>   sections: authors
#>    authors (n=9): nested list
#> 
#> 
#> $elife
#> $elife$`10.7554/eLife.03032`
#> <pub chunks>
#>   from: xml_document
#>   sections: authors
#>    authors (n=6): nested list
#> 
#> 
#> attr(,"ft_data")
#> [1] TRUE


Tabularize

It’s great to pull out the sections you want, but most people will likely want to work with data.frame’s instead of lists. pub_tabularize is the answer:

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

It handles many inputs as well:

out <- pub_chunks(
  list(pensoft_xml, peerj_xml, copernicus_xml, frontiers_xml),
  sections = c("doi", "title", "keywords")
)
pub_tabularize(out)
#> [[1]]
#>                                                                                                     title
#> 1 Contribution to the knowledge of seed-beetles (Coleoptera, Chrysomelidae, Bruchinae) in Xinjiang, China
#>   .publisher
#> 1    pensoft
#> 
#> [[2]]
#>                                                                                                title
#> 1 Storm effects on intertidal invertebrates: increased beta diversity of few individuals and species
#>   .publisher
#> 1      peerj
#> 
#> [[3]]
#>                      doi
#> 1 10.5194/asr-12-23-2015
#>                                                     title .publisher
#> 1 Quality control of 10-min soil temperatures data at RMI copernicus
#> 
#> [[4]]
#>                        doi
#> 1 10.3389/fmicb.2012.00403
#>                                                        title .publisher
#> 1 Metagenomic Analysis of a Southern Maritime Antarctic Soil  frontiers

The output of pub_tabularize is a list of data.frame’s. You can easily combine the output with e.g. rbind or data.table::rbindlist or dplyr::bind_rows. Here’s an example with data.table::rbindlist:

data.table::rbindlist(pub_tabularize(out), fill = TRUE)
#>                                                                                                      title
#> 1: Contribution to the knowledge of seed-beetles (Coleoptera, Chrysomelidae, Bruchinae) in Xinjiang, China
#> 2:      Storm effects on intertidal invertebrates: increased beta diversity of few individuals and species
#> 3:                                                 Quality control of 10-min soil temperatures data at RMI
#> 4:                                              Metagenomic Analysis of a Southern Maritime Antarctic Soil
#>    .publisher                      doi
#> 1:    pensoft                     <NA>
#> 2:      peerj                     <NA>
#> 3: copernicus   10.5194/asr-12-23-2015
#> 4:  frontiers 10.3389/fmicb.2012.00403


TO DO

We’ll be adding support for more publishers (including right now working on Pubmed XML format articles), more article sections, making sure default section extraction is smart as possible, and more.

Of course, if you know XPATH and don’t mind doing it, you can do what this package does yourself. However, you will have to write different XPATH for different publishers/journals, so leveraging this approach still may save some time.