esummary: esummary
In gschofl/rentrez: An R interface to the NCBI EUtilities

Description Usage Arguments Details Value Class hierarchy for esummary Generics with methods for esummary Slots Examples

“esummary” is an S4 class that provides a container for data retrived by calls to the NCBI ESummary utility.

esummary retrieves 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).

1 2	esummary(id, db = NULL, retstart = 1, retmax = 10000, query_key = NULL, WebEnv = NULL, version = "2.0")

`id`	(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 `esearch`, `epost` or `elink`. If UIDs are provided as a plain character vector, `db` must be specified explicitly, and all of the UIDs must be from the database specified by `db`.
`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).
`query_key`	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`, `epost` or `elink` calls.)
`WebEnv`	A character string specifying the Web Environment that contains the UID list. (Usually obtained directely from objects returned by previous `esearch`, `epost` or `elink` calls.)
`version`	If "2.0" `esummary` will retrieve version 2.0 ESummary XML output.

See the official online documentation for NCBI's EUtilities for additional information.

An esummary instance.

Super classes:

eutil

[
[[
content
database
docsum
show

url: A character vector containing the query URL.
error: Any error or warning messages parsed from the output of the call submitted to Entrez.
content: A character vector holding the unparsed contents of a request to Entrez.
database: The name of the queried database.
version: The version of the document summary requested.
docsum: The parsed document summaries for a list of input UIDs.

## Downloading Document Summaries ##########################################

# Download DocSums for some protein GIs: 313848131,313847824,313847819,
# 313847818,313847817

id <- c(313848131,313847824,313847819,313847818,313847817)
doc <- esummary(id, "protein")

# Download data from a previous ESearch.
s <- esearch(term="evolution and ecology", db="journals", usehistory=TRUE)
doc <- esummary(s)

# Retrieve the docsum as a data frame or as the XML response.
ds <- docsum(doc)
ds[["Title"]]

ds_xml <- content(doc, "xml")

# Get accession numbers for a list of GIs
id <- c(313848131, 313847824, 313847819, 313847818, 313847817)
prot <- docsum(esummary(id, "protein"))
names(prot)
prot[, c("Id","Caption","Slen","TaxId")]