reutils (version 0.1.1)

esummary: esummary - downloading Document Summaries

Description

esummary performs calls to the NCBI ESummary utility to retrieve document summaries (DocSums) for a list of primary UIDs or for a set of UIDs stored in the user's web environment (using the Entrez History server).

Usage

esummary(uid, db = NULL, retstart = 1, retmax = 10000, querykey = NULL,
  webenv = NULL, version = "2.0")

Arguments

uid

(Required) List of UIDs provided either as a character vector, as an esearch or elink object, or by reference to a Web Environment and a query key obtained directly from objects returned by previous calls to

db

(Required only when id is a character vector of UIDs) Database from which to retrieve DocSums.

retstart

Numeric index of the first DocSum to be retrieved (default: 1).

retmax

Total number of DocSums from the input set to be retrieved (maximum: 10,000).

querykey

An integer specifying which of the UID lists attached to a user's Web Environment will be used as input to efetch. (Usually obtained drectely from objects returned by previous esearch,

webenv

A character string specifying the Web Environment that contains the UID list. (Usually obtained directely from objects returned by previous esearch, epost

version

If "2.0" esummary will retrieve version 2.0 ESummary XML output.

Value

• An esummary object.

Details

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

See Also

content, getUrl, getError, database.

Examples

## Retrieve the Document Summary information for a set of
## UIDs frome the Gene datanase.
ds <- esummary(c("828392", "790", "470338"), "gene")

## parse the XML into a data frame
df <- content(ds, "parsed")
df

## use XPath expressions to extract nodes of interest
ds['//TaxID']