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fulltext

Full Text of 'Scholarly' Articles Across Many Data Sources

Provides a single interface to many sources of full text 'scholarly' data, including 'Biomed Central', Public Library of Science, 'Pubmed Central', 'eLife', 'F1000Research', 'PeerJ', 'Pensoft', 'Hindawi', 'arXiv' 'preprints', and more. Functionality included for searching for articles, downloading full or partial text, downloading supplementary materials, converting to various data formats.

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cran checks Project Status: Active – The project has reached a stable, usable state and is being actively developed. Build Status codecov.io rstudio mirror downloads cran version

Get full text articles from lots of places

Checkout 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:

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

Article full text formats by publisher: https://github.com/ropensci/fulltext/blob/master/vignettes/formats.Rmd

Stable version from CRAN

install.packages("fulltext")

Development version from GitHub

devtools::install_github("ropensci/fulltext")

Load library

library('fulltext')

Search

ft_search() - get metadata on a search query.

ft_search(query = 'ecology', from = 'crossref')
#> Query:
#>   [ecology] 
#> Found:
#>   [PLoS: 0; BMC: 0; Crossref: 157839; Entrez: 0; arxiv: 0; biorxiv: 0; Europe PMC: 0; Scopus: 0; Microsoft: 0] 
#> Returned:
#>   [PLoS: 0; BMC: 0; Crossref: 10; Entrez: 0; arxiv: 0; biorxiv: 0; Europe PMC: 0; Scopus: 0; Microsoft: 0]

Get full text links

ft_links() - get links for articles (xml and pdf).

res1 <- ft_search(query = 'biology', from = 'entrez', limit = 5)
ft_links(res1)
#> <fulltext links>
#> [Found] 5 
#> [IDs] ID_30253098 ID_28731711 ID_28097372 ID_27582426 ID_22243231 ...

Or pass in DOIs directly

ft_links(res1$entrez$data$doi, from = "entrez")
#> <fulltext links>
#> [Found] 5 
#> [IDs] ID_30253098 ID_28731711 ID_28097372 ID_27582426 ID_22243231 ...

Get full text

ft_get() - get full or partial text of articles.

ft_get('10.7717/peerj.228')
#> <fulltext text>
#> [Docs] 1 
#> [Source] ext - /Users/sckott/Library/Caches/R/fulltext 
#> [IDs] 10.7717/peerj.228 ...

Extract chunks

library(pubchunks)
x <- ft_get(c('10.7554/eLife.03032', '10.7554/eLife.32763'), from = "elife")
x %>% ft_collect() %>% pub_chunks("publisher") %>% pub_tabularize()
#> $elife
#> $elife$`10.7554/eLife.03032`
#>                          publisher .publisher
#> 1 eLife Sciences Publications, Ltd      elife
#> 
#> $elife$`10.7554/eLife.32763`
#>                          publisher .publisher
#> 1 eLife Sciences Publications, Ltd      elife

Get multiple fields at once

x %>% ft_collect() %>% pub_chunks(c("doi","publisher")) %>% pub_tabularize()
#> $elife
#> $elife$`10.7554/eLife.03032`
#>                   doi                        publisher .publisher
#> 1 10.7554/eLife.03032 eLife Sciences Publications, Ltd      elife
#> 
#> $elife$`10.7554/eLife.32763`
#>                   doi                        publisher .publisher
#> 1 10.7554/eLife.32763 eLife Sciences Publications, Ltd      elife

Pull out the data.frame's

x %>%
  ft_collect() %>% 
  pub_chunks(c("doi", "publisher", "author")) %>%
  pub_tabularize() %>%
  .$elife
#> $`10.7554/eLife.03032`
#>                   doi                        publisher authors.given_names
#> 1 10.7554/eLife.03032 eLife Sciences Publications, Ltd                  Ya
#>   authors.surname authors.given_names.1 authors.surname.1
#> 1            Zhao                 Jimin               Lin
#>   authors.given_names.2 authors.surname.2 authors.given_names.3
#> 1               Beiying                Xu                  Sida
#>   authors.surname.3 authors.given_names.4 authors.surname.4
#> 1                Hu                   Xue             Zhang
#>   authors.given_names.5 authors.surname.5 .publisher
#> 1                Ligang                Wu      elife
#> 
#> $`10.7554/eLife.32763`
#>                   doi                        publisher authors.given_names
#> 1 10.7554/eLife.32763 eLife Sciences Publications, Ltd             Natasha
#>   authors.surname authors.given_names.1 authors.surname.1
#> 1          Mhatre                Robert            Malkin
#>   authors.given_names.2 authors.surname.2 authors.given_names.3
#> 1                Rittik               Deb                Rohini
#>   authors.surname.3 authors.given_names.4 authors.surname.4 .publisher
#> 1      Balakrishnan                Daniel            Robert      elife

Extract text from PDFs

There are going to be cases in which some results you find in ft_search() have full text available in text, xml, or other machine readable formats, but some may be open access, but only in pdf format. We have a series of convenience functions in this package to help extract text from pdfs, both locally and remotely.

Locally, using code adapted from the package tm, and two pdf to text parsing backends

pdf <- system.file("examples", "example2.pdf", package = "fulltext")
ft_extract(pdf)
#> <document>/Library/Frameworks/R.framework/Versions/3.5/Resources/library/fulltext/examples/example2.pdf
#>   Title: pone.0107412 1..10
#>   Producer: Acrobat Distiller 9.0.0 (Windows); modified using iText 5.0.3 (c) 1T3XT BVBA
#>   Creation date: 2014-09-18

Interoperability with other packages downstream

cache_options_set(path = (td <- 'foobar'))
#> $cache
#> [1] TRUE
#> 
#> $backend
#> [1] "ext"
#> 
#> $path
#> [1] "/Users/sckott/Library/Caches/R/foobar"
#> 
#> $overwrite
#> [1] FALSE
res <- ft_get(c('10.7554/eLife.03032', '10.7554/eLife.32763'), type = "pdf")
library(readtext)
x <- readtext::readtext(file.path(cache_options_get()$path, "*.pdf"))
library(quanteda)
quanteda::corpus(x)
#> Corpus consisting of 2 documents and 0 docvars.

Contributors

Meta

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

rofooter

News

fulltext 1.2.0

NEW FEATURES

  • ft_get() gains a progress parameter, TRUE printing a progress bar and FALSE not. By default we do not print a progress bar to be consistent with the behavior of previous versions (#140) (#190)
  • cache_options_set() gains new parameter full_path to set the entire path to the cache, use like cache_options_set(full_path = yourpath) (#185) thanks @bomeara for the feature request

DEFUNCT

BUG FIXES

  • Fix to eupmc_search() internal function. At some piont Europe PMC changed the way they do paging, what parameters are used, etc. Fixed now. See examples for how to do paging; uses a cursor model instead of a rows/offset model (#184) thanks @jshleap for the report
  • two hopefully fixes for Wiley URLs: a) try a 2nd url pattern if the first fails in general for Wiley links; and b) if highwire links found, replace with a url pattern that should work (#189) thanks @bomeara for the report

NEW IMPROVEMENTS

  • remaining httr code removed, now using crul for all HTTP requests (#187)
  • filled out Scopus and Crossref TDM parts in the Authentication section of the package level manual file ?fulltext-package; and add more details on authentication in the ?ft_get manual file (#182) (#183)

fulltext 1.1.0

NEW FEATURES

  • gains new function cache_file_info() to get information on possibly bad files in your cache - which you can use to remove files as you see fit (#142) (#174) thx @lucymerobinson for the push
  • gains new function as.ft_data() to create the same output as ft_get() returns, but instead pulls all files from your cache (#142) (#172) thanks @lucymerobinson
  • ft_get() gains new attribute of a data.frame in the errors slot with information on each article and what error we collected or NA_character_ if none; should help with sorting out problems across all requests (#176)
  • scopus option in ft_search() gains support for facets; see ?scopus_search (#170) thanks @lucymerobinson

BUG FIXES

  • fixed bug in ft_search() for microsoft academic plugin (#154)
  • fixed bug in ft_search() for scopus plugin - we weren't looping over requests correctly (#161)
  • fix bug in ft_links() - when result of ft_search() passed to ft_links with bad urls or with more than 1 then ft_links was failing; fix by filtering on intended-application field from Crossref via fix in dependency package crminer (#173)
  • additional check added in ft_get() to check for an invalid file that gave a 200 status code (so passes the status code check) (#175)
  • bring back support for start parameter in ft_search() for Scopus to offset what record a query starts at (#180)
  • fix to ft_get() for entrez data source to loop internally when more than 50 ids requested to avoid 414 http error (URI too long) (#167) thanks @t088

MINOR IMPROVEMENTS

  • change base url for EuropePMC to https
  • use https for all doi.org requests (#155) thanks @katrinleinweber
  • better explanation of the may opts parameters in ft_search() (#161)
  • after many attempts, finally (I think) sorted out Microbiology Society for the ft_get() function (#163) thanks to @low-decarie
  • mention suppdata package in the README (#164)
  • clarify language in ft_collect() that we are saving files to disk locally only (#165)
  • fix typos (#166) (#168) thanks @maelle @AugustT
  • removed whisker package dependency (#156)
  • scopus gains support for more parameters; see ?scopus_search (#152)
  • updated docs with information on using NCBI Entrez API keys (#159)
  • plugin for publisher Instituto de Investigaciones Filologicas to ft_get() added (#117) thanks @andreifoldes
  • clarified in ft_search() docs that for some sources we loop internally to get whatever number of records the user wants, while others we can not (#162)

DEPRECATED

Continuing to focus the scope of this package the functions ft_chunks() and ft_tabularize() are now deprecated, and will be removed (defunct) in a future version of this package. See the new package https://github.com/ropensci/pubchunks for the same and better functionality. (#181)

fulltext 1.0.1

BUG FIXES

  • Fix bug in internal function get_ext() which parses either xml, pdf, or plain text from files on disk - it was failing on Linux maxchines due to a faulty regex (#151)

MINOR IMPROVEMENTS

  • Updated formats vignette, three publishers that used to provide XML no longer do (#150)

fulltext 1.0

Check out the fulltext manual for detailed documentation.

fulltext has undergone a re-organization, which includes a bump in the major version to v1 to reinforce the large changes the package has undergone. Changes include:

  • Function name standardization with the ft_ prefix. e,g, chunks is now ft_chunks
  • ft_get has undergone major re-organization - biggest of which may be that all full text XML/plain text/PDF goes to disk to simplify the user interface.
  • storr is now imported to manage mapping between real DOIs and file paths that include normalized DOIs - and aids in the function ft_table() for creating a data.frame of text results
  • Note that with the ft_get() overhaul, the only option is to write to disk. Before we attempted to provide many different options for saving XML and PDF data, but it was too complicated. This has implications for using the output of ft_get() - the output is only the paths to the files - use ft_collect() to collect the text if you want to use ft_chunks() or other fulltext functions downstream.

NEW FEATURES

  • chunks changed to ft_chunks (#139)
  • collect changed to ft_collect (#139)
  • tabularize changed to ft_tabularize (#139)
  • get_text changed to ft_text (#139)
  • ft_get() gains new parameter try_unknown that attempts to try to find full text for a given DOI/ID even if we don't have code plugins specifically for that publisher. This includes trying to get a full text link from Crossref and the https://ftdoi.org API (#137)
  • Gains function ft_table that outputs a data.frame of all downloaded articles with DOIs, filenames, and the text of each article, similar to the readtext package (#134)
  • Gains function ft_abstract for fetching abstracts, including support for getting abstracts from Scopus, Microsoft Academic, Crossref, and PLOS (#98) (#115)
  • Microsoft Academic added as another data source both in ft_abstract and in ft_search via the microdemic package (#99) (#115)
  • ft_get() gains an S3 method for ft_links - that is, you can pass the output of ft_links() to ft_get() (#103)
  • ft_get() gains many new plugins, including for: Informa, Scientific Societies, Europe PMC, Elsevier, Wiley, xxx (#121) (#112) (#52) (#96) (#120) (#xxx)
  • Gains new functions to list available plugins for each of ft_get()/ft_links()/ft_search(): ft_get_ls()/ft_links_ls()/ft_search_ls() (#122)
  • ft_chunks() gains support for Elsevier XML (#116) (#118)
  • Scopus added as a new datasource in both ft_search() and ft_abstract (#95)
  • gains new object ftxt_cache for managing/listing details of cached files from ft_get()
  • ft_search() gains Scopus and Microsoft Academic options
  • ft_serialize() loses file, rcache, and redis options, retaining options for converting between list, JSON, and XML formats.
  • The package level manual file at ?fulltext-package gains new sections on authentication and rate limiting
  • gains new manual file for how to interpret warnings when using ft_get(); see ?ft_get-warnings

DEFUNCT

With the re-focusing of the package these functions seemed out of scope, so have been removed:

  • pdfx, pdfx_html, and pdfx_targz are now defunct (#145)
  • ft_extract_corpus is now defunct

The following functions have changed names. Usually I'd mark functions as deprecated in a version, then defunct in the next version, but since we're moving to v1 here, it made sense to rip the bandade off and make the old function names defunct.

  • chunks is now defunct - function name changed to ft_chunks
  • tabularize is now defunct - function name changed to ft_tabularize
  • collect is now defunct - function name changed to ft_collect
  • get_text is now defunct - function name changed to ft_text

Other defunct:

  • cache_clear was never working anyway, and is now removed.

Along with the above changes and others the packages R.cache, rredis, digest, and tm have been removed from Imports

MINOR IMPROVEMENTS

  • Replaced httr with crul mostly throughtout the package (#104)
  • We are now using DOIs in file names written to disk from ft_get(). DOIs are normalized before using to create file paths (#138)
  • Output of ft_get() should now be correctly named lists after the publisher and the DOI/ID (#126)
  • Switched for eLife DOIs to attempt to get full text links from Crossref API instead of constructing by hand (#127)
  • Now using hoardr package for managing cached files (#124)
  • sending user agent string for this R pkg to the ftdoi.org API when calling it now (#141)
  • Documented option to include your email address with Crossref API queries to get in their "fast lane" (#123)
  • Documented how to get rate limit headers/information for Elsevier/Scopus requests (#109)
  • For text extraction from PDFs - only using pdftools now - done away with other options (#82)
  • biorxiv_search is now exported but the man file is hidden (using roxygen2 directive @internal), so you can still get to the manual file doing ?biorxiv_search

BUG FIXES

  • New internal PLOS API method instead of a function from rplos because we need to write to disk instead of return parsed XML output (#148)
  • ft_get() now appropriately using cached version of file if found (#130)
  • The type parameter in ft_get() was ignored previously, now definitely used. (#128)
  • Fix biorxiv_search (#97) (#113)

fulltext 0.1.8

MINOR IMPROVEMENTS

  • require newest rcrossref and rplos versions that use dplyr::bind_rows() instead of dplyr::rbind_all() to avoid errors/warnings (#89) (#90)

fulltext 0.1.6

MINOR IMPROVEMENTS

  • More documentation added for the from parameter for ft_get_si() to clarify its use, and fails better when used inappropriately (#68) (#77)
  • ft_get_si() now gives file type information as attributes so that downstream uses can access that information instead of having to guess file types (#69)

BUG FIXES

  • Fixes to ft_get_si() to work with changes in the publisher Wiley's URL changes (#71) (#73)

fulltext 0.1.4

NEW FEATURES

  • New function ft_get_si() to grab supplementary files for any article (#61) (#62) - thanks @willpearse
  • New function ft_links() to grab links for the full text version of an article from entire output of ft_search(), their individual components (i.e., data sources), or from character vector of DOIs (#36)

MINOR IMPROVEMENTS

  • Lowercased all column headers from ft_search() (#63)
  • DRYed out plugins for ft_get() to reduce code duplication (#48)

BUG FIXES

  • Fixed bug in ft_search() where limit integer was too big (#57)
  • Fix to ft_get() to create a directory if it doesn't exist already (#56)
  • Fixed bug in ft_search() that caused problems in some scenarios (#55)
  • Better error message when pdf passed to pdfx() function when pdf is not useable, that is, e.g., a scanned pdf (#53)

fulltext 0.1.0

  • Released to CRAN.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.
install.packages("fulltext")

1.7.0 by Scott Chamberlain, 2 months ago

https://docs.ropensci.org/fulltext/ (website) https://github.com/ropensci/fulltext/ (devel) https://books.ropensci.org/fulltext/ (user manual)

Report a bug at https://github.com/ropensci/fulltext/issues

Browse source code at https://github.com/cran/fulltext

Authors: Scott Chamberlain [aut, cre] , rOpenSci [fnd] (https://ropensci.org/)

Documentation:   PDF Manual  

Task views: Web Technologies and Services

MIT + file LICENSE license

Imports crul, magrittr, xml2, jsonlite, rplos, rcrossref, microdemic, aRxiv, rentrez, data.table, hoardr, pdftools, storr, tibble, digest, fauxpas

Suggests roxygen2, testthat, pubchunks, vcr

Suggested by pubchunks, rotl, suppdata.

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