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Get links to datasets related to records from an NCBI database

Source: R/entrez_link.r
entrez_link.Rd

Discover records related to a set of unique identifiers from an NCBI database. The object returned by this function depends on the value set for the cmd argument. Printing the returned object lists the names , and provides a brief description, of the elements included in the object.

Usage

entrez_link(
  dbfrom,
  web_history = NULL,
  id = NULL,
  db = NULL,
  cmd = "neighbor",
  by_id = FALSE,
  config = NULL,
  ...
)

Arguments

dbfrom

character Name of database from which the Id(s) originate

web_history

a web_history object

id

vector with unique ID(s) for records in database db.

db

character Name of the database to search for links (or use "all" to search all databases available for db. entrez_db_links allows you to discover databases that might have linked information (see examples).

cmd

link function to use. Allowed values include

  • neighbor (default). Returns a set of IDs in db linked to the input IDs in dbfrom.

  • neighbor_score. As `neighbor”, but additionally returns similarity scores.

  • neighbor_history. As `neighbor', but returns web history objects.

  • acheck. Returns a list of linked databases available from NCBI for a set of IDs.

  • ncheck. Checks for the existence of links within a single database.

  • lcheck. Checks for external (i.e. outside NCBI) links.

  • llinks. Returns a list of external links for each ID, excluding links provided by libraries.

  • llinkslib. As 'llinks' but additionally includes links provided by libraries.

  • prlinks. As 'llinks' but returns only the primary external link for each ID.

by_id

logical If FALSE (default) return a single elink objects containing links for all of the provided ids. Alternatively, if TRUE return a list of elink objects, one for each ID in id.

config

vector configuration options passed to httr::GET

...

character Additional terms to add to the request, see NCBI documentation linked to in references for a complete list

Value

An elink object containing the data defined by the cmd argument (if by_id=FALSE) or a list of such object (if by_id=TRUE).

file XMLInternalDocument xml file resulting from search, parsed with xmlTreeParse

References

https://www.ncbi.nlm.nih.gov/books/NBK25499/#_chapter4_ELink_

See also

config for available configs

entrez_db_links

Examples

if (FALSE) { # \dontrun{
 pubmed_search <- entrez_search(db = "pubmed", term ="10.1016/j.ympev.2010.07.013[doi]")
 linked_dbs <- entrez_db_links("pubmed")
 linked_dbs
 nucleotide_data <- entrez_link(dbfrom = "pubmed", id = pubmed_search$ids, db ="nuccore")
 #Sources for the full text of the paper 
 res <- entrez_link(dbfrom="pubmed", db="", cmd="llinks", id=pubmed_search$ids)
 linkout_urls(res)
} # }