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

Description Usage Arguments Details Value Class hierarchy for esearch Generics with methods for esearch Slots See Also Examples

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

esearch searches and retrieves primary UIDs matching a text query for use with efetch, esummary, and elink. esearch can post its output set of UIDs to the Entrez history server if the usehistory parameter is set TRUE. The resulting esearch object can be passed on to esummary, efetch, or elink.

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

`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 stored directly in the user's Web environment so that they can be used in a subsequent call to `esummary`, `efetch`, or `elink`. Also, `usehistory` must be set to `TRUE` for `esearch` to interpret query key values included in `term` or to accept a `WebEnv` as input.
`WebEnv`	Web environment string returned by a previous call to `esearch`, `epost` or `elink`. When provided, `esearch` will append the results of the search to the pre-existing WebEnv. Providing WebEnv also allows query keys to be used in `term` so that previous search sets can be combined or limited.
`query_key`	query key returned by a previous call to `esearch`, `epost` or `elink`. When provided, `esearch` will find the intersection of the set specified by query_key and the set retrieved by the query in `term` (i.e. joins the two with AND).
`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.

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

An esearch instance.

Super classes:

eutil

[
content
count
database
idList
length
queryKey
queryTranslation
retmax
retstart
show
webEnv

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.
idList: An object of class idList

esummary, efetch, elink

## Basic searching #########################################################

# Get th PubMed IDs (PMIDs) for articles about Chlamydia psittaci
# that have been published in 2011.

cpsit <- esearch(term="Chlamydia psittaci and 2011[pdat]", db="pubmed")
cpsit

# Search in PubMed for articles published by the journal PNAS in Volume 97.

pnas <- esearch(term="PNAS[jour] and 97[vol]", db="pubmed")
pnas

# Search for protein UIDs corresponding to BRCA1 in humans.
# To ensure that we retrieve the full list of IDs, we count
# the number of hits to set the 'retmax' parameter.

query <- "BRCA1 and human"
n <- count(esearch(query, "protein", rettype="count"))
brca1 <- esearch(query, "protein", retmax=n)

## Storing search results on the Entrez history server #####################

query <- "BRCA1 and human"
brca1 <- esearch(query, "protein", retmax=2443, usehistory=TRUE)
brca1