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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/entrez_search.r
\name{entrez_search}
\alias{entrez_search}
\title{Search the NCBI databases using EUtils}
\usage{
entrez_search(
db,
term,
config = NULL,
retmode = "xml",
use_history = FALSE,
...
)
}
\arguments{
\item{db}{character, name of the database to search for.}
\item{term}{character, the search term. The syntax used in making these
searches is described in the Details of this help message, the package
vignette and reference given below.}
\item{config}{vector configuration options passed to httr::GET}
\item{retmode}{character, one of json (default) or xml. This will make no
difference in most cases.}
\item{use_history}{logical. If TRUE return a web_history object for use in
later calls to the NCBI}
\item{\dots}{character, additional terms to add to the request, see NCBI
documentation linked to in references for a complete list}
}
\value{
ids integer Unique IDS returned by the search
count integer Total number of hits for the search
retmax integer Maximum number of hits returned by the search
web_history A web_history object for use in subsequent calls to NCBI
QueryTranslation character, search term as the NCBI interpreted it
file either and XMLInternalDocument xml file resulting from search, parsed with
\code{\link[XML]{xmlTreeParse}} or, if \code{retmode} was set to json a list
resulting from the returned JSON file being parsed with
\code{\link[jsonlite]{fromJSON}}.
}
\description{
Search a given NCBI database with a particular query.
}
\details{
The NCBI uses a search term syntax where search terms can be associated with
a specific search field with square brackets. So, for instance ``Homo[ORGN]''
denotes a search for Homo in the ``Organism'' field. The names and
definitions of these fields can be identified using
\code{\link{entrez_db_searchable}}.
Searches can make use of several fields by combining them via the boolean
operators AND, OR and NOT. So, using the search term``((Homo[ORGN] AND APP[GENE]) NOT
Review[PTYP])'' in PubMed would identify articles matching the gene APP in
humans, and exclude review articles. More examples of the use of these search
terms, and the more specific MeSH terms for precise searching,
is given in the package vignette. \code{rentrez} handles special characters
and URL encoding (e.g. replacing spaces with plus signs) on the client side,
so there is no need to include these in search term
The\code{rentrez} tutorial provides some tips on how to make the most of
searches to the NCBI. In particular, the sections on uses of the "Filter"
field and MeSH terms may in formulating precise searches.
}
\examples{
\dontrun{
query <- "Gastropoda[Organism] AND COI[Gene]"
web_env_search <- entrez_search(db="nuccore", query, use_history=TRUE)
cookie <- web_env_search$WebEnv
qk <- web_env_search$QueryKey
snail_coi <- entrez_fetch(db = "nuccore", WebEnv = cookie, query_key = qk,
file_format = "fasta", retmax = 10)
}
\dontrun{
fly_id <- entrez_search(db="taxonomy", term="Drosophila")
#Oh, right. There is a genus and a subgenus name Drosophila...
#how can we limit this search
(tax_fields <- entrez_db_searchable("taxonomy"))
#"RANK" loots promising
tax_fields$RANK
entrez_search(db="taxonomy", term="Drosophila & Genus[RANK]")
}
}
\references{
\url{https://www.ncbi.nlm.nih.gov/books/NBK25499/#_chapter4_ESearch_}
}
\seealso{
\code{\link[httr]{config}} for available httr configurations
\code{\link{entrez_db_searchable}} to get a set of search fields that
can be used in \code{term} for any database
}
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