identify open content license urls used for open access articles in hybrid journals

[njahn82]

Here's a reproducible example (reprex) to obtain licenses used for all hybrid journals covered by the Open APC initiative.

# required libraries
library(dplyr) # data transformation
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(tidyr) # working with list-columns
library(jsonlite) # working with json files
# load data, most recent dump, which also includes data from Jan and Feb 2020
license_df <- jsonlite::stream_in(url("https://raw.githubusercontent.com/subugoe/hybrid_oa_dashboard/update_jan_feb_20/data/jn_facets_df.json"), verbose = FALSE)
# prepare a summary table, where all license URLs´s variants are broken down by publisher
license_df %>%
  select(license_refs, journal_title, publisher) %>%
  unnest(license_refs) %>%
  # unterschiedliche Fälle je Verlag
  group_by(.id, publisher) %>%
  summarise(n_cases = sum(V1)) 
#> # A tibble: 567 x 3
#> # Groups:   .id [216]
#>    .id                                    publisher                 n_cases
#>    <chr>                                  <chr>                       <int>
#>  1 http:// creativecommons.org/licenses/… Cambridge University Pre…       3
#>  2 http://academic.oup.com/journals/page… Elsevier BV                     1
#>  3 http://academic.oup.com/journals/page… Oxford University Press …    4734
#>  4 http://academic.oup.com/journals/page… Oxford University Press …      23
#>  5 http://aspb.org/publications/aspb-jou… American Society of Plan…    4039
#>  6 http://avs.scitation.org/jvb/authors/… American Vacuum Society        35
#>  7 http://creative commons.org/licenses/… Cambridge University Pre…       1
#>  8 http://creative commons.org/licenses/… Cambridge University Pre…       1
#>  9 http://creative commons.org/licenses/… Cambridge University Pre…       1
#> 10 http://creative%20commons.org/license… Cambridge University Pre…       2
#> # … with 557 more rows

^{Created on 2020-03-06 by the reprex package (v0.3.0)}

[njahn82]

Some background:

Existing White List
https://github.com/subugoe/hybrid_oa_dashboard/blob/8e1e50d9403ec90a94c699e51919a46aeb1c0418/R/cr_fetching.R#L192-L203

Existing script to harmonize license urls https://github.com/subugoe/hybrid_oa_dashboard/blob/8e1e50d9403ec90a94c699e51919a46aeb1c0418/R/license_normalise.R#L4-L20

Related approach with comprehensive White List: “Applying Crossref and Unpaywall information to identify gold, hidden gold, hybrid and delayed Open Access publications in the KB publication corpus”: https://osf.io/preprints/socarxiv/sdzft/

[njahn82]

Filtering journals where no license urls were shared using the keep_empty = TRUE param from tidyr::unnest()

# required libraries
library(dplyr) # data transformation
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(tidyr) # working with list-columns
library(jsonlite) # working with json files
# load data, most recent dump, which also includes data from Jan and Feb 2020
license_df <- jsonlite::stream_in(url("https://raw.githubusercontent.com/subugoe/hybrid_oa_dashboard/update_jan_feb_20/data/jn_facets_df.json"), verbose = FALSE)
# prepare a summary table, where all license URLs´s variants are broken down by publisher
license_df %>%
  select(license_refs, journal_title, publisher) %>%
  unnest(license_refs, keep_empty =TRUE) %>%
  filter(is.na(.id))
#> # A tibble: 470 x 4
#>    .id      V1 journal_title                     publisher                 
#>    <chr> <int> <chr>                             <chr>                     
#>  1 <NA>     NA Natures Sciences Sociétés         EDP Sciences              
#>  2 <NA>     NA Journal of Neuroscience           Society for Neuroscience  
#>  3 <NA>     NA Genes & Development               Cold Spring Harbor Labora…
#>  4 <NA>     NA Physiological Genomics            American Physiological So…
#>  5 <NA>     NA Climate Research                  Inter-Research Science Ce…
#>  6 <NA>     NA Jahrbuch der Österreichischen By… Osterreichische Akademie …
#>  7 <NA>     NA Zeitschrift für Antikes Christen… Walter de Gruyter GmbH    
#>  8 <NA>     NA Journal of Lipid Research         American Society for Bioc…
#>  9 <NA>     NA Molecular Biology of the Cell     American Society for Cell…
#> 10 <NA>     NA Journal of Biological Chemistry   American Society for Bioc…
#> # … with 460 more rows

^{Created on 2020-03-19 by the reprex package (v0.3.0)}

[maxheld83]

I haven't touched any of this substantively, but I've created some scaffolding in 8e3cc1e.
I think the functions mentioned above to parse/corall/summarise the licensing info should be documented in the same place.

license_patterns is currently a static data frame, but once the above is implemented it should probably be re-evaluated on every build time (though not run time).
It might then have to be a function as per #47.