rorcid is an R programmatic interface to the Orcid public API. rorcid is not a product developed or distributed by ORCID®.

Orcid API docs:

The package now works with the v3.0 ORCID API. It’s too complicated to allow users to work with different versions of the API, so it’s hard-coded to v3.0.

Authentication

There are two ways to authenticate with rorcid:

  • Use a token as a result of a OAuth authentication process. The token is a alphanumeric UUID, e.g. dc0a6b6b-b4d4-4276-bc89-78c1e9ede56e. You can get this token by running orcid_auth(), then storing that key (the uuid alone, not the “Bearer” part) either as en environment variable called ORCID_TOKEN in your .Renviron file in your home directory, or as an R option in your .Rprofile file (called orcid_token). See ?Startup for more information. Either an environment variable or R option work. If we don’t find either we do the next option.
  • Interactively login with OAuth. We use a client id and client secret key to ping ORCID.org; at which point you log in with your username/password; then we get back a token (same as the above option). We don’t know your username or password, only the token that we get back. We cache that token locally in a hidden file in whatever working directory you’re in. If you delete that file, or run the code from a new working directory, then we re-authorize.

We recommend the former option. That is, get a token and store it as an environment variable.

If both options above fail, we proceed without using authentication. ORCID does not require authentication at this point, but may in the future - this prepares you for when that happens :)

See https://members.orcid.org/api/oauth/orcid-scopes for more about ORCID OAuth Scopes.

Computing environments without browsers

One pitfall is when you are using rorcid on a server, and you’re ssh’ed in, so that there’s no way to open a browser to do the OAuth browser flow. Similarly for any other situation in which a browser can not be opened. In this case, run orcid_auth() on another machine in which you do have the ability to open a browser, then collect the info that’s ouptput from orcid_auth() and store it as an environment variable (see above).

Installation

Stable version

Development version

remotes::install_github("ropensci/rorcid")
library('rorcid')

as.orcid

There’s a function as.orcid() in this package to help coerce an Orcid ID to an object that holds details for that Orcid ID, prints a nice summary, and you can browse easily to that profile. E.g.

as.orcid(x = "0000-0002-1642-628X")
#> <ORCID> 0000-0002-1642-628X
#>   Name: Boettiger, Carl
#>   URL (first): http://www.carlboettiger.info
#>   Country: US
#>   Keywords: Ecology, Evolution, Regime Shifts, Stochastic Dynamics

Or you can pass in many IDs

as.orcid(c("0000-0003-1620-1408", "0000-0002-9341-7985"))
#> [[1]]
#> <ORCID> 0000-0003-1620-1408
#>   Name: Johnson, Thomas
#>   URL (first): 
#>   Country: US
#>   Keywords: 
#> 
#> [[2]]
#> <ORCID> 0000-0002-9341-7985
#>   Name: Binfield, Peter
#>   URL (first): 
#>   Country: US
#>   Keywords:

The browse() function lets you browser to a profile easily with a single function call

browse(as.orcid("0000-0002-1642-628X"))

profile

Get works

The works() function helps get works data from an orcid data object. The output of works() is a data.frame

(out <- works(orcid_id("0000-0002-0233-1757")))
#> # A tibble: 6 x 32
#>   `put-code` url   type  `journal-title` visibility path  `display-index`
#> *      <int> <lgl> <chr> <lgl>           <chr>      <chr> <chr>          
#> 1    5296064 NA    jour… NA              public     /000… 0              
#> 2    5296065 NA    jour… NA              public     /000… 0              
#> 3    5296066 NA    jour… NA              public     /000… 0              
#> 4    9012984 NA    jour… NA              public     /000… 0              
#> 5    9012985 NA    jour… NA              public     /000… 0              
#> 6    9012986 NA    jour… NA              public     /000… 0              
#> # … with 25 more variables: `created-date.value` <dbl>,
#> #   `last-modified-date.value` <dbl>, `source.source-client-id` <lgl>,
#> #   `source.assertion-origin-orcid` <lgl>,
#> #   `source.assertion-origin-client-id` <lgl>,
#> #   `source.assertion-origin-name` <lgl>, `source.source-orcid.uri` <chr>,
#> #   `source.source-orcid.path` <chr>, `source.source-orcid.host` <chr>,
#> #   `source.source-name.value` <chr>, title.subtitle <lgl>,
#> #   `title.translated-title` <lgl>, title.title.value <chr>,
#> #   `external-ids.external-id` <list>, `publication-date.year.value` <chr>,
#> #   `publication-date.month.value` <chr>, `publication-date.day.value` <chr>,
#> #   `publication-date.day` <lgl>, `external-ids` <lgl>,
#> #   `publication-date` <lgl>, `source.source-orcid` <lgl>,
#> #   `source.source-client-id.uri` <chr>, `source.source-client-id.path` <chr>,
#> #   `source.source-client-id.host` <chr>, url.value <chr>

Search Orcid

Get a list of names and Orcid IDs matching a name query

orcid(query = "carl boettiger")
#> # A tibble: 1,000 x 3
#>    `orcid-identifier.uri`            `orcid-identifier.pa… `orcid-identifier.ho…
#>  * <chr>                             <chr>                 <chr>                
#>  1 https://orcid.org/0000-0002-1642… 0000-0002-1642-628X   orcid.org            
#>  2 https://orcid.org/0000-0002-3554… 0000-0002-3554-5196   orcid.org            
#>  3 https://orcid.org/0000-0002-5951… 0000-0002-5951-4503   orcid.org            
#>  4 https://orcid.org/0000-0003-1853… 0000-0003-1853-1574   orcid.org            
#>  5 https://orcid.org/0000-0002-7462… 0000-0002-7462-1956   orcid.org            
#>  6 https://orcid.org/0000-0002-7790… 0000-0002-7790-5102   orcid.org            
#>  7 https://orcid.org/0000-0003-1021… 0000-0003-1021-5374   orcid.org            
#>  8 https://orcid.org/0000-0001-8899… 0000-0001-8899-7850   orcid.org            
#>  9 https://orcid.org/0000-0001-9705… 0000-0001-9705-4766   orcid.org            
#> 10 https://orcid.org/0000-0001-7084… 0000-0001-7084-5402   orcid.org            
#> # … with 990 more rows

You can string together many search terms

orcid(query = "johnson cardiology houston")
#> # A tibble: 1,000 x 3
#>    `orcid-identifier.uri`            `orcid-identifier.pa… `orcid-identifier.ho…
#>  * <chr>                             <chr>                 <chr>                
#>  1 https://orcid.org/0000-0002-0897… 0000-0002-0897-2301   orcid.org            
#>  2 https://orcid.org/0000-0002-5281… 0000-0002-5281-4466   orcid.org            
#>  3 https://orcid.org/0000-0001-8188… 0000-0001-8188-0078   orcid.org            
#>  4 https://orcid.org/0000-0002-2862… 0000-0002-2862-4160   orcid.org            
#>  5 https://orcid.org/0000-0002-0682… 0000-0002-0682-9982   orcid.org            
#>  6 https://orcid.org/0000-0002-4334… 0000-0002-4334-4001   orcid.org            
#>  7 https://orcid.org/0000-0001-9667… 0000-0001-9667-1615   orcid.org            
#>  8 https://orcid.org/0000-0003-4792… 0000-0003-4792-0149   orcid.org            
#>  9 https://orcid.org/0000-0003-0945… 0000-0003-0945-6138   orcid.org            
#> 10 https://orcid.org/0000-0001-5156… 0000-0001-5156-0356   orcid.org            
#> # … with 990 more rows

And use boolean operators

orcid("johnson AND(caltech OR 'California Institute of Technology')")
#> # A tibble: 1,000 x 3
#>    `orcid-identifier.uri`            `orcid-identifier.pa… `orcid-identifier.ho…
#>  * <chr>                             <chr>                 <chr>                
#>  1 https://orcid.org/0000-0002-0026… 0000-0002-0026-2516   orcid.org            
#>  2 https://orcid.org/0000-0002-3710… 0000-0002-3710-1070   orcid.org            
#>  3 https://orcid.org/0000-0002-3909… 0000-0002-3909-2294   orcid.org            
#>  4 https://orcid.org/0000-0002-5340… 0000-0002-5340-8347   orcid.org            
#>  5 https://orcid.org/0000-0002-7705… 0000-0002-7705-5670   orcid.org            
#>  6 https://orcid.org/0000-0002-7443… 0000-0002-7443-1546   orcid.org            
#>  7 https://orcid.org/0000-0001-6495… 0000-0001-6495-9892   orcid.org            
#>  8 https://orcid.org/0000-0003-4199… 0000-0003-4199-0314   orcid.org            
#>  9 https://orcid.org/0000-0003-0758… 0000-0003-0758-2296   orcid.org            
#> 10 https://orcid.org/0000-0002-7042… 0000-0002-7042-5739   orcid.org            
#> # … with 990 more rows

And you can use start and rows arguments to do pagination

orcid("johnson cardiology houston", start = 2, rows = 3)
#> # A tibble: 3 x 3
#>   `orcid-identifier.uri`            `orcid-identifier.pat… `orcid-identifier.ho…
#> * <chr>                             <chr>                  <chr>                
#> 1 https://orcid.org/0000-0001-8188… 0000-0001-8188-0078    orcid.org            
#> 2 https://orcid.org/0000-0002-2862… 0000-0002-2862-4160    orcid.org            
#> 3 https://orcid.org/0000-0002-0682… 0000-0002-0682-9982    orcid.org

Search by Orcid ID

out <- orcid_id(orcid = "0000-0002-9341-7985")
out$`0000-0002-9341-7985`$name
#> $`created-date`
#> $`created-date`$value
#> [1] 1.460762e+12
#> 
#> 
#> $`last-modified-date`
#> $`last-modified-date`$value
#> [1] 1.460762e+12
#> 
#> 
#> $`given-names`
#> $`given-names`$value
#> [1] "Peter"
#> 
#> 
#> $`family-name`
#> $`family-name`$value
#> [1] "Binfield"
#> 
#> 
#> $`credit-name`
#> NULL
#> 
#> $source
#> NULL
#> 
#> $visibility
#> [1] "public"
#> 
#> $path
#> [1] "0000-0002-9341-7985"

Search by DOIs

There is a helper function check_dois() that uses a regex checker to see if your DOIs are likely good or likely bad:

All good DOIs

dois <- c("10.1371/journal.pone.0025995","10.1371/journal.pone.0053712",
       "10.1371/journal.pone.0054608","10.1371/journal.pone.0055937")
check_dois(dois)
#> $good
#> [1] "10.1371/journal.pone.0025995" "10.1371/journal.pone.0053712"
#> [3] "10.1371/journal.pone.0054608" "10.1371/journal.pone.0055937"
#> 
#> $bad
#> NULL

Some good, some bad

dois <- c("10.1016/j.medpal.2008.12.005","10.1080/00933104.2000.10505926","10.1037/a0024480",
        "10.1002/anie.196603172","2344","asdf","232","asdf","23dd")
check_dois(dois)
#> $good
#> [1] "10.1016/j.medpal.2008.12.005"   "10.1080/00933104.2000.10505926"
#> [3] "10.1037/a0024480"               "10.1002/anie.196603172"        
#> 
#> $bad
#> [1] "2344" "asdf" "232"  "asdf" "23dd"

Basic search

orcid_doi(dois = "10.1087/20120404")
#> [[1]]
#> # A tibble: 14 x 3
#>    `orcid-identifier.uri`            `orcid-identifier.pa… `orcid-identifier.ho…
#>  * <chr>                             <chr>                 <chr>                
#>  1 https://orcid.org/0000-0002-3181… 0000-0002-3181-3456   orcid.org            
#>  2 https://orcid.org/0000-0002-1290… 0000-0002-1290-9735   orcid.org            
#>  3 https://orcid.org/0000-0001-7343… 0000-0001-7343-9784   orcid.org            
#>  4 https://orcid.org/0000-0003-3738… 0000-0003-3738-1487   orcid.org            
#>  5 https://orcid.org/0000-0001-5727… 0000-0001-5727-2427   orcid.org            
#>  6 https://orcid.org/0000-0003-0187… 0000-0003-0187-9064   orcid.org            
#>  7 https://orcid.org/0000-0003-1603… 0000-0003-1603-8743   orcid.org            
#>  8 https://orcid.org/0000-0002-2123… 0000-0002-2123-6317   orcid.org            
#>  9 https://orcid.org/0000-0002-0860… 0000-0002-0860-8606   orcid.org            
#> 10 https://orcid.org/0000-0003-0493… 0000-0003-0493-0128   orcid.org            
#> 11 https://orcid.org/0000-0003-3188… 0000-0003-3188-6273   orcid.org            
#> 12 https://orcid.org/0000-0002-5993… 0000-0002-5993-8592   orcid.org            
#> 13 https://orcid.org/0000-0003-1419… 0000-0003-1419-2405   orcid.org            
#> 14 https://orcid.org/0000-0001-5109… 0000-0001-5109-3700   orcid.org            
#> 
#> attr(,"class")
#> [1] "orcid_doi"

This DOI is not a real one, but a partial DOI, then we can fuzzy search

orcid_doi(dois = "10.1087/2", fuzzy = TRUE, rows = 5)
#> [[1]]
#> # A tibble: 5 x 3
#>   `orcid-identifier.uri`            `orcid-identifier.pat… `orcid-identifier.ho…
#> * <chr>                             <chr>                  <chr>                
#> 1 https://orcid.org/0000-0001-8701… 0000-0001-8701-615X    orcid.org            
#> 2 https://orcid.org/0000-0001-6081… 0000-0001-6081-0708    orcid.org            
#> 3 https://orcid.org/0000-0001-5919… 0000-0001-5919-8670    orcid.org            
#> 4 https://orcid.org/0000-0002-0634… 0000-0002-0634-3376    orcid.org            
#> 5 https://orcid.org/0000-0001-8959… 0000-0001-8959-3380    orcid.org            
#> 
#> attr(,"class")
#> [1] "orcid_doi"

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