Open access copies of scholarly publications are sometimes hard to find. Some are published in open access journals. Others are made freely available as preprints before publication, and others are deposited in institutional repositories, digital archives maintained by universities and research institutions. This document guides you to roadoi, a R client that makes it easy to search for these open access copies by interfacing the ourresearch service where DOIs are matched with freely available full-texts available from open access journals and archives.
Unpaywall, developed and maintained by the team of ourresearch, is a non-profit service that finds open access copies of scholarly literature simply by looking up a DOI (Digital Object Identifier). It not only returns open access full-text links, but also helpful metadata about the open access status of a publication such as licensing or provenance information.
Unpaywall uses different data sources to find open access full-texts including:
See Piwowar et al. (2018) for a comprehensive overview of Unpaywall.
There is one major function to talk with Unpaywall, oadoi_fetch(), taking a character vector of DOIs and your email address as required arguments.
library(roadoi)
roadoi::oadoi_fetch(dois = c("10.1186/s12864-016-2566-9",
"10.1103/physreve.88.012814"),
email = "najko.jahn@gmail.com")## # A tibble: 2 x 21
## doi best_oa_location oa_locations oa_locations_em… data_standard is_oa
## <chr> <list> <list> <list> <int> <lgl>
## 1 10.1… <tibble [1 × 10… <tibble [6 … <tibble [0 × 0]> 2 TRUE
## 2 10.1… <tibble [1 × 10… <tibble [2 … <tibble [0 × 0]> 2 TRUE
## # … with 15 more variables: is_paratext <lgl>, genre <chr>, oa_status <chr>,
## # has_repository_copy <lgl>, journal_is_oa <lgl>, journal_is_in_doaj <lgl>,
## # journal_issns <chr>, journal_issn_l <chr>, journal_name <chr>,
## # publisher <chr>, published_date <chr>, year <chr>, title <chr>,
## # updated_resource <chr>, authors <list>The client supports API version 2. According to the Unpaywall Data Format, the following variables with the following definitions are returned:
| Column | Description |
|---|---|
doi |
DOI (always in lowercase) |
best_oa_location |
list-column describing the best OA location. Algorithm prioritizes publisher hosted content (e.g. Hybrid or Gold) |
oa_locations |
list-column of all the OA locations. |
oa_locations_embargoed |
list-column of locations expected to be available in the future based on information like license metadata and journals’ delayed OA policies |
data_standard |
Indicates the data collection approaches used for this resource. 1 mostly uses Crossref for hybrid detection. 2 uses more comprehensive hybrid detection methods. |
is_oa |
Is there an OA copy (logical)? |
is_paratext |
Is the item an ancillary part of a journal, like a table of contents? See here for more information https://support.unpaywall.org/support/solutions/articles/44001894783. |
genre |
Publication type |
oa_status |
Classifies OA resources by location and license terms as one of: gold, hybrid, bronze, green or closed. See here for more information https://support.unpaywall.org/support/solutions/articles/44001777288-what-do-the-types-of-oa-status-green-gold-hybrid-and-bronze-mean-. |
has_repository_copy |
Is a full-text available in a repository? |
journal_is_oa |
Is the article published in a fully OA journal? Uses the Directory of Open Access Journals (DOAJ) as source. |
journal_is_in_doaj |
Is the journal listed in the Directory of Open Access Journals (DOAJ). |
journal_issns |
ISSNs, i.e. unique code to identify journals. |
journal_issn_l |
Linking ISSN. |
journal_name |
Journal title |
publisher |
Publisher |
published_date |
Date published |
year |
Year published. |
title |
Publication title. |
updated_resource |
Time when the data for this resource was last updated. |
authors |
Lists authors (if available) |
The columns best_oa_location and oa_locations are list-columns that contain useful metadata about the OA sources found by Unpaywall These are
| Column | Description |
|---|---|
endpoint_id |
Unique repository identifier |
evidence |
How the OA location was found and is characterized by Unpaywall? |
host_type |
OA full-text provided by publisher or repository. |
is_best |
Is this location the for its resource? |
license |
The license under which this copy is published |
oa_date |
When this document first became available at this location |
pmh_id |
OAI-PMH endpoint where we found this location |
repository_institution |
Hosting institution of the repository. |
updated |
Time when the data for this location was last updated |
url |
The URL where you can find this OA copy. |
url_for_landing_page |
The URL for a landing page describing this OA copy. |
url_for_pdf |
The URL with a PDF version of this OA copy. |
versions |
The content version accessible at this location following the DRIVER 2.0 Guidelines (https://wiki.surfnet.nl/display/DRIVERguidelines/DRIVER-VERSION+Mappings) |
The Unpaywall schema is also described here: https://unpaywall.org/data-format.
The columns best_oa_location. oa_locations and oa_locations_embargoed are list-columns that contain useful metadata about the OA sources found by Unpaywall.
If .flatten = TRUE the list-column oa_locations will be restructured in a long format where each OA fulltext is represented by one row, which allows to take into account all OA locations found by Unpaywall in a data analysis.
library(dplyr)##
## Attaching package: 'dplyr'## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, unionroadoi::oadoi_fetch(dois = c("10.1186/s12864-016-2566-9",
"10.1103/physreve.88.012814",
"10.1093/reseval/rvaa038",
"10.1101/2020.05.22.111294",
"10.1093/bioinformatics/btw541"),
email = "najko.jahn@gmail.com", .flatten = TRUE) %>%
dplyr::count(is_oa, evidence, is_best) ## # A tibble: 8 x 4
## is_oa evidence is_best n
## <lgl> <chr> <lgl> <int>
## 1 FALSE <NA> NA 1
## 2 TRUE oa journal (via doaj) FALSE 1
## 3 TRUE oa repository (semantic scholar lookup) FALSE 1
## 4 TRUE oa repository (via OAI-PMH doi match) FALSE 7
## 5 TRUE oa repository (via page says license) TRUE 1
## 6 TRUE oa repository (via pmcid lookup) FALSE 2
## 7 TRUE open (via crossref license, author manuscript) TRUE 1
## 8 TRUE open (via page says license) TRUE 2There are no API restrictions. However, Unpaywall requires an email address when using its API. If you are too tired to type in your email address every time, you can store the email in the .Renviron file with the option roadoi_email
roadoi_email = "najko.jahn@gmail.com"You can open your .Renviron file calling
file.edit("~/.Renviron")`Save the file and restart your R session. To stop sharing the email when using roadoi, delete it from your .Renviron file.
To follow your API call, and to estimate the time until completion, use the .progress parameter inherited from plyr to display a progress bar.
roadoi::oadoi_fetch(dois = c("10.1186/s12864-016-2566-9",
"10.1103/physreve.88.012814"),
email = "najko.jahn@gmail.com",
.progress = "text")##
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%## # A tibble: 2 x 21
## doi best_oa_location oa_locations oa_locations_em… data_standard is_oa
## <chr> <list> <list> <list> <int> <lgl>
## 1 10.1… <tibble [1 × 10… <tibble [6 … <tibble [0 × 0]> 2 TRUE
## 2 10.1… <tibble [1 × 10… <tibble [2 … <tibble [0 × 0]> 2 TRUE
## # … with 15 more variables: is_paratext <lgl>, genre <chr>, oa_status <chr>,
## # has_repository_copy <lgl>, journal_is_oa <lgl>, journal_is_in_doaj <lgl>,
## # journal_issns <chr>, journal_issn_l <chr>, journal_name <chr>,
## # publisher <chr>, published_date <chr>, year <chr>, title <chr>,
## # updated_resource <chr>, authors <list>An increasing number of universities, research organisations and funders have launched open access policies in recent years. Using roadoi together with other R-packages allows to examine how and to what extent researchers comply with these policies in a reproducible and transparent manner. In particular, the rcrossref package, maintained by rOpenSci, provides many helpful functions for this task.
DOIs have become essential for referencing scholarly publications, and thus many digital libraries and institutional databases keep track of these persistent identifiers. For the sake of this vignette, instead of starting with a pre-defined set of publications originating from these sources, we simply generate a random sample of 50 articles published in the Journal of the Association for Information Science and Technology from Crossref with the rcrossref package.
library(dplyr)
library(rcrossref)
# get a random sample of DOIs and metadata describing these works
random_dois <- rcrossref::cr_r(filter = list(
issn = "2330-1643", type = "journal-article"
), sample = 50)Now let’s call Unpaywall and store the results in oa_df:
oa_df <- roadoi::oadoi_fetch(random_dois,
email = "najko.jahn@gmail.com")roadoi returns the data in a consistent structure improved for further analysis in R.
oa_df## # A tibble: 50 x 21
## doi best_oa_location oa_locations oa_locations_em… data_standard is_oa
## <chr> <list> <list> <list> <int> <lgl>
## 1 10.1… <tibble [1 × 12… <tibble [2 … <tibble [1 × 13… 2 TRUE
## 2 10.1… <tibble [0 × 0]> <tibble [0 … <tibble [0 × 0]> 2 FALSE
## 3 10.1… <tibble [0 × 0]> <tibble [0 … <tibble [0 × 0]> 2 FALSE
## 4 10.1… <tibble [1 × 8]> <tibble [1 … <tibble [0 × 0]> 2 TRUE
## 5 10.1… <tibble [1 × 10… <tibble [2 … <tibble [0 × 0]> 2 TRUE
## 6 10.1… <tibble [0 × 0]> <tibble [0 … <tibble [0 × 0]> 2 FALSE
## 7 10.1… <tibble [0 × 0]> <tibble [0 … <tibble [0 × 0]> 2 FALSE
## 8 10.1… <tibble [1 × 11… <tibble [1 … <tibble [0 × 0]> 2 TRUE
## 9 10.1… <tibble [0 × 0]> <tibble [0 … <tibble [0 × 0]> 2 FALSE
## 10 10.1… <tibble [1 × 11… <tibble [1 … <tibble [0 × 0]> 2 TRUE
## # … with 40 more rows, and 15 more variables: is_paratext <lgl>, genre <chr>,
## # oa_status <chr>, has_repository_copy <lgl>, journal_is_oa <lgl>,
## # journal_is_in_doaj <lgl>, journal_issns <chr>, journal_issn_l <chr>,
## # journal_name <chr>, publisher <chr>, published_date <chr>, year <chr>,
## # title <chr>, updated_resource <chr>, authors <list>For example, to determine how many full-text links were found and which sources were used:
oa_df %>%
group_by(is_oa) %>%
summarise(Articles = n()) %>%
mutate(Proportion = Articles / sum(Articles)) %>%
arrange(desc(Articles))## `summarise()` ungrouping output (override with `.groups` argument)## # A tibble: 2 x 3
## is_oa Articles Proportion
## <lgl> <int> <dbl>
## 1 FALSE 30 0.6
## 2 TRUE 20 0.4How did Unpaywall find those Open Access full-texts, and which were characterized as best matches?
oa_df %>%
filter(is_oa == TRUE) %>%
tidyr::unnest(oa_locations) %>%
group_by(oa_status, evidence, is_best) %>%
summarise(Articles = n()) %>%
arrange(desc(Articles))## `summarise()` regrouping output by 'oa_status', 'evidence' (override with `.groups` argument)## # A tibble: 10 x 4
## # Groups: oa_status, evidence [9]
## oa_status evidence is_best Articles
## <chr> <chr> <lgl> <int>
## 1 bronze open (via free article) TRUE 8
## 2 green oa repository (via OAI-PMH doi match) TRUE 5
## 3 hybrid oa repository (via OAI-PMH doi match) FALSE 4
## 4 hybrid open (via crossref license) FALSE 4
## 5 hybrid open (via page says license) TRUE 4
## 6 green oa repository (via OAI-PMH title and first author… FALSE 3
## 7 green oa repository (via OAI-PMH title and first author… TRUE 3
## 8 bronze oa repository (via OAI-PMH doi match) FALSE 1
## 9 bronze oa repository (via OAI-PMH title match) FALSE 1
## 10 hybrid oa repository (via pmcid lookup) FALSE 1For more examples, see Piwowar et al. 2018. Together with the article, the authors shared their analysis of Unpaywall Data as R Markdown supplement.
This blog post describes how to analyze the Unpaywall data dump with R: https://subugoe.github.io/scholcomm_analytics/posts/unpaywall_evidence/
Piwowar, H., Priem, J., Larivière, V., Alperin, J. P., Matthias, L., Norlander, B., … Haustein, S. (2018). The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles. PeerJ, 6, e4375. https://doi.org/10.7717/peerj.4375