add_publication_from_unpaywall: Add a publication or preprint to the publication table via...
In nf-osi/nfportalutils: NF Portal Utilities

View source: R/add_publication_from_unpaywall.R

add_publication_from_unpaywall

R Documentation

Add a publication or preprint to the publication table via the Unpaywall API.

Description

Add a publication to the publication table. Publication must be in unpaywall database to retrieve info. For parameter-provided metadata (e.g. "studyName"), function must a JSON-formatted character vector if the destination Synapse column is of "STRING_LIST" format. Currently, this function does not evaluate the schema, so this must be checked manually.

Usage

add_publication_from_unpaywall(
  publication_table_id,
  email_address,
  doi,
  is_preprint = F,
  preprint_server = NULL,
  study_name,
  study_id,
  funding_agency,
  disease_focus,
  manifestation,
  dry_run = T
)

Arguments

`publication_table_id`	The synapse id of the portal publication table. Must have write access.
`email_address`	A valid email address. Is used to request metadata from the Unpaywall API. Please change the example to a real email address to help Unpaywall accurately track usage.
`doi`	The DOI of the preprint to be added.
`is_preprint`	Default = FALSE. Set to TRUE if DOI is from a preprint.
`preprint_server`	Provide preprint server name. Must be one of 'bioRxiv', 'medRxiv', 'chemRxiv', 'arXiv'
`study_name`	The name(s) of the study that are associated with the publication.
`study_id`	The synapse id(s) of the study that are associated with the publication.
`funding_agency`	The funding agency(s) that are associated with the publication.
`disease_focus`	The disease focus(s) that are associated with the publication.
`manifestation`	The manifestation(s) that are associated with the publication.
`dry_run`	Default = TRUE. Skips upload to table and instead prints formatted publication metadata.

Value

If dry_run == T, returns publication metadata to be added.

Examples

## Not run: 
add_publication_from_unpaywall(publication_table_id = 'syn16857542',
               email_address = 'foo@bar.com',
               doi = '10.1074/jbc.RA120.014960',
               study_name = c(toJSON("Synodos NF2")),
               study_id = c(toJSON("syn2343195")),
               funding_agency = c(toJSON("CTF")),
               disease_focus = "Neurofibromatosis 2",
               manifestation = c(toJSON("Meningioma")),
               dry_run = T)

## End(Not run)

nf-osi/nfportalutils documentation built on Feb. 26, 2024, 1:05 p.m.