reutils (version 0.1.1)

elink: elink - finding related data through Entrez links

Description

elink generates a list of UIDs in a specified Entrez database that are linked to a set of input UIDs in either the same or another database. For instance, the ELink utility can find Entrez gene records linked to records in Entrez Protein.

Usage

elink(uid, dbFrom = NULL, dbTo = NULL, linkname = NULL,
  usehistory = FALSE, cmd = "neighbor", correspondence = FALSE,
  querykey = NULL, webenv = NULL, term = NULL, holding = NULL,
  datetype = NULL, reldate = NULL, mindate = NULL, maxdate = NULL)

Arguments

uid

(Required) A character vector of UIDs.

dbFrom

Initial database containing the UIDs in the input list.

dbTo

Destination database from which to retrieve linked UIDs. If not provided links will be sought in the database containing the input UIDs.

linkname

Name of the Entrez link to retrieve. Every link in Entrez is given a name of the form dbFrom_dbTo_subset.

usehistory

If TRUE search results are stored directly in the user's Web environment so that they can be used in subsequents calls to esummary or efetch

cmd

ELink command mode (default: 'neighbor'). See Details.

correspondence

if TRUE correspondence between query UIDs and destination UIDs is preserved.

querykey

Query key.

webenv

Web Environment.

term

Search query to limit the output set of linked UIDs.

holding

Name of LinkOut provider.

datetype

Type of date to limit the search. One of 'mdat' (modification date), 'pdat' (publication date) or 'edat' (Entrez date).

reldate

umber of days back for which search items are returned.

mindate

Minimum date of search range. Format YYYY/MM/DD.

maxdate

Maximum date of search range. Format YYYY/MM/DD.

Value

• An elink object.

Details

See the official online documentation for NCBI's http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ELink{EUtilities} for additional information.

If dbTo and dbFrom are set to the same database, ELink will return neighbors within that database.

Elink commands (cmd) specify the function that elink will perform. Available commands are:

• "neighbor"

{(Default) ELink returns a set of UIDs in dbTo linked to the input UIDs in dbFrom.} "neighbor_score"{ELink returns a set of UIDs within the same database as the input UIDs along with similarity scores.} "neighbor_history"{ELink posts the output UIDs to the Entrez History server and returns a query_key and WebEnv parameter. Alternatively this is achieved by setting usehistory=TRUE}

See Also

Combine calls to ELink with other EUtils: esummary, efetch.

Accessor methods: content, getUrl, getError, database, uid, linkset,

Examples

## Find one set of Gene IDs linked to nuccore GIs 34577062 and 24475906
e <- elink(c("34577062", "24475906"), dbFrom="nuccore", dbTo="gene")
e

## Find related articles to PMID 20210808
p <- elink("20210808", dbFrom="pubmed", dbTo="pubmed")
p

## Extract linked UIDs from the "pubmed" to "pubmed_reviews" link
linkset(p, "pubmed_pubmed_reviews")

## or
p["pubmed_pubmed_reviews"]

## retrive the abstracts for the first five linked reviews
abstracts <- efetch(p["pubmed_pubmed_reviews"][1:5], rettype="abstract")