R: Get links to datasets related to records from an NCBI...

entrez_link {rentrez} | R Documentation

## Get links to datasets related to records from an NCBI database

### Description

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 `id`s. 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

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

### See Also

`config` for available configs

`entrez_db_links`

### Examples

     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)

[Package rentrez version 1.2.1 Index]