add_publication_from_pubmed: Add a publication to the publication table

In nf-osi/nfportalutils: NF Portal Utilities

Add a publication to the publication table

Description

Requires that the publication be in PubMed to auto-derive metadata such as authors, title, etc. In contrast, disease_focus and manifestation need to be supplemented by the curator. The study_id is used to get consistent studyName and fundingAgency from study table without manual input.

Usage

add_publication_from_pubmed(
  pmid,
  study_id,
  disease_focus,
  manifestation,
  publication_table_id,
  study_table_id,
  dry_run = T
)

Arguments

pmid	PubMed ID (not PMCID) of the publication to be added.
study_id	Synapse id(s) of the study 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.
publication_table_id	Synapse id of the portal publication table. Must have write access.
study_table_id	Synapse id of the portal study table. Need read access.
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_pubmed(
               pmid = "33574490",
               study_id = "syn2343195",
               disease_focus = c("Neurofibromatosis"),
               manifestation = c("Meningioma"),
               publication_table_id = "syn16857542",
               study_table_id = "syn16787123")

## End(Not run)

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