reutils (version 0.1.1)

esearch: esearch - searching an Entrez database

Description

esearch performs searches using the the NCBI ESearch utility to retrieve primary UIDs matching a text query. These UIDs can be used in subsequent calls to esummary, efetch, or elink.

Usage

esearch(term, db = "nuccore", rettype = "uilist", retstart = 0,
  retmax = 100, usehistory = FALSE, webenv = NULL, querykey = NULL,
  field = NULL, datetype = NULL, reldate = NULL, mindate = NULL,
  maxdate = NULL)

Arguments

term

A valid Entrez text query.

db

Database to search (default: nuccore).

rettype

Retrieval type. (default: 'uilist', alternative: 'count'.)

retstart

Numeric index of the first UID in the retrieved set to be shown in the XML output (default: 0).

retmax

Total number of UIDs to be retrieved (default: 100).

usehistory

If TRUE, search results are posted directly to the Entrez History Server so that they can be used in subsequent calls to esummary, efetch,

webenv

Web environment string returned by a previous call to esearch, epost or elink. When provided, esearc

querykey

query key returned by a previous call to esearch, epost or elink. When provided, esearch will

field

Optional. Search field used to limit the entire search term.

datetype

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

reldate

Optional. Number of days back for which search items are returned.

mindate

Optional. Minimum date of search range. Format YYYY/MM/DD, YYYY/MM, or YYYY.

maxdate

Optional. Maximum date of search range. Format YYYY/MM/DD, YYYY/MM, or YYYY.

Value

• An esearch object.

Details

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

See Also

Combine calls to ESearch with other EUtils: esummary, efetch, elink.

Accessor methods: content, getUrl, getError, database, uid, webenv, querykey.

Examples

## Search PubMed for articles with the term "Chlamydia psittaci" in the
## title that were published in 2013.
pmid <- esearch("Chlamydia psittaci[titl] and 2013[pdat]", "pubmed")
pmid

## Extract the query results either as an XML tree or parsed into
## a character vector
xml <- content(pmid, "xml")
uids <- uid(pmid)

## Alternatively post the UIDs to the History Server.
pmid <- esearch("Chlamydia psittaci[titl] and 2013[pdat]", "pubmed", usehistory=TRUE)
pmid

## Associate new search results with the existing search results.
pmid2 <- esearch("Chlamydia psittaci[titl] and 2012[pdat]", "pubmed",
                 usehistory=TRUE, webenv=webenv(pmid))
pmid2