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Examples · Estimated reading time: 10 minutes

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/
esearch.fcgi?db=<database>&term=<query>
esearch.fcgi?db=<database>&term=<query>&usehistory=y
esearch.fcgi?db=<database>&term=<query1>&usehistory=y

# esearch produces WebEnv value ($web1) and QueryKey value ($key1) 

esearch.fcgi?db=<database>&term=<query2>&usehistory=y&WebEnv=$web1

# esearch produces WebEnv value ($web2) that contains the results 
of both searches ($key1 and $key2)
<?xml version="1.0" ?>
<!DOCTYPE eSearchResult PUBLIC "-//NLM//DTD eSearchResult, 11 May 2002//EN"
 "https://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd">
<eSearchResult>
<Count>255147</Count>   # total number of records matching query
<RetMax>20</RetMax># number of UIDs returned in this XML; default=20
<RetStart>0</RetStart># index of first record returned; default=0
<QueryKey>1</QueryKey># QueryKey, only present if &usehistory=y
<WebEnv>0l93yIkBjmM60UBXuvBvPfBIq8-9nIsldXuMP0hhuMH-
8GjCz7F_Dz1XL6z@397033B29A81FB01_0038SID</WebEnv> 
                  # WebEnv; only present if &usehistory=y
      <IdList>
<Id>229486465</Id>    # list of UIDs returned
<Id>229486321</Id>
<Id>229485738</Id>
<Id>229470359</Id>
<Id>229463047</Id>
<Id>229463037</Id>
<Id>229463022</Id>
<Id>229463019</Id>
<Id>229463007</Id>
<Id>229463002</Id>
<Id>229463000</Id>
<Id>229462974</Id>
<Id>229462961</Id>
<Id>229462956</Id>
<Id>229462921</Id>
<Id>229462905</Id>
<Id>229462899</Id>
<Id>229462873</Id>
<Id>229462863</Id>
<Id>229462862</Id>
</IdList>
<TranslationSet>        # details of how Entrez translated the query
    <Translation>
     <From>mouse[orgn]</From>
     <To>"Mus musculus"[Organism]</To>
    </Translation>
</TranslationSet>
<TranslationStack>
   <TermSet>
    <Term>"Mus musculus"[Organism]</Term>
    <Field>Organism</Field>
    <Count>255147</Count>
    <Explode>Y</Explode>
   </TermSet>
   <OP>GROUP</OP>
</TranslationStack>
<QueryTranslation>"Mus musculus"[Organism]</QueryTranslation>
</eSearchResult>
ecitmatch.cgi?db=pubmed&rettype=xml&bdata=<citations>
proc natl acad sci u s a|1991|88|3248|mann bj|Art1|2014248
science|1987|235|182|palmenberg ac|Art2|3026048
epost.fcgi?db=<database>&id=<uid_list>
epost.fcgi?db=<database1>&id=<uid_list1>

# epost produces WebEnv value ($web1) and QueryKey value ($key1)

epost.fcgi?db=<database2>&id=<uid_list2>&WebEnv=$web1

# epost produces WebEnv value ($web2) that contains the results of both 
posts ($key1 and $key2)
<?xml version="1.0"?>
<!DOCTYPE ePostResult PUBLIC "-//NLM//DTD ePostResult, 11 May 2002//EN"
 "https://www.ncbi.nlm.nih.gov/entrez/query/DTD/ePost_020511.dtd">
<ePostResult>
<QueryKey>1</QueryKey>
<WebEnv>NCID_01_268116914_130.14.18.47_9001_1241798628</WebEnv>
</ePostResult>
esummary.fcgi?db=<database>&id=<uid_list>
esearch.fcgi?db=<database>&term=<query>&usehistory=y

# esearch produces WebEnv value ($web1) and QueryKey value ($key1)

esummary.fcgi?db=<database>&query_key=$key1&WebEnv=$web1
<?xml version="1.0"?>
<!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD eSummaryResult, 29 October
 2004//EN" "https://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSummary_
041029.dtd">
<eSummaryResult>
<DocSum>
<Id>15718680</Id>
<Item Name="Caption" Type="String">NP_005537</Item>
<Item Name="Title" Type="String">IL2-inducible T-cell kinase [Homo
 sapiens]</Item>
<Item Name="Extra" 
Type="String">gi|15718680|ref|NP_005537.3|[15718680]</Item>
<Item Name="Gi" Type="Integer">15718680</Item>
<Item Name="CreateDate" Type="String">1999/06/09</Item>
<Item Name="UpdateDate" Type="String">2009/04/05</Item>
<Item Name="Flags" Type="Integer">512</Item>
<Item Name="TaxId" Type="Integer">9606</Item>
<Item Name="Length" Type="Integer">620</Item>
<Item Name="Status" Type="String">live</Item>
<Item Name="ReplacedBy" Type="String"></Item>
<Item Name="Comment" Type="String"><![CDATA[  ]]></Item>
</DocSum>
</eSummaryResult>
esummary.fcgi?db=<database>&id=<uid_list>&version=2.0
<?xml version="1.0"?>
<!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD eSummaryResult//EN" "https://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSummaryDTD/eSummary_protein.dtd">
<eSummaryResult>
    <DocumentSummarySet status="OK">
        <DocumentSummary uid="15718680">
            <Caption>NP_005537</Caption>
            <Title>tyrosine-protein kinase ITK/TSK [Homo sapiens]</Title>
            <Extra>gi|15718680|ref|NP_005537.3|</Extra>
            <Gi>15718680</Gi>

            <CreateDate>1999/06/09</CreateDate>
            <UpdateDate>2011/10/09</UpdateDate>
            <Flags>512</Flags>
            <TaxId>9606</TaxId>
            <Slen>620</Slen>

            <Biomol/>

            <MolType>aa</MolType>
            <Topology>linear</Topology>
            <SourceDb>refseq</SourceDb>
            <SegSetSize>0</SegSetSize>
            <ProjectId>0</ProjectId>
            <Genome>genomic</Genome>

            <SubType>chromosome|map</SubType>
            <SubName>5|5q31-q32</SubName>
            <AssemblyGi>399658</AssemblyGi>
            <AssemblyAcc>D13720.1</AssemblyAcc>
            <Tech/>
            <Completeness/>
            <GeneticCode>1</GeneticCode>

            <Strand/>
            <Organism>Homo sapiens</Organism>
            <Statistics>
                <Stat type="all" count="8"/>
                <Stat type="blob_size" count="16154"/>
                <Stat type="cdregion" count="1"/>
                <Stat type="cdregion" subtype="CDS" count="1"/>
                <Stat type="gene" count="1"/>
                <Stat type="gene" subtype="Gene" count="1"/>
                <Stat type="org" count="1"/>
                <Stat type="prot" count="1"/>
                <Stat type="prot" subtype="Prot" count="1"/>
                <Stat type="pub" count="14"/>
                <Stat type="pub" subtype="PubMed" count="10"/>
                <Stat type="pub" subtype="PubMed/Gene-rif" count="4"/>
                <Stat type="site" count="4"/>
                <Stat type="site" subtype="Site" count="4"/>
                <Stat source="CDD" type="all" count="15"/>
                <Stat source="CDD" type="region" count="6"/>
                <Stat source="CDD" type="region" subtype="Region" count="6"/>
                <Stat source="CDD" type="site" count="9"/>
                <Stat source="CDD" type="site" subtype="Site" count="9"/>
                <Stat source="HPRD" type="all" count="3"/>
                <Stat source="HPRD" type="site" count="3"/>
                <Stat source="HPRD" type="site" subtype="Site" count="3"/>
                <Stat source="SNP" type="all" count="31"/>
                <Stat source="SNP" type="imp" count="31"/>
                <Stat source="SNP" type="imp" subtype="variation" count="31"/>
                <Stat source="all" type="all" count="57"/>
                <Stat source="all" type="blob_size" count="16154"/>
                <Stat source="all" type="cdregion" count="1"/>
                <Stat source="all" type="gene" count="1"/>
                <Stat source="all" type="imp" count="31"/>
                <Stat source="all" type="org" count="1"/>
                <Stat source="all" type="prot" count="1"/>
                <Stat source="all" type="pub" count="14"/>
                <Stat source="all" type="region" count="6"/>
                <Stat source="all" type="site" count="16"/>
            </Statistics>
            <AccessionVersion>NP_005537.3</AccessionVersion>
            <Properties aa="2">2</Properties>
            <Comment/>
            <OSLT indexed="yes">NP_005537.3</OSLT>
            <IdGiClass mol="3" repr="2" gi_state="10" sat="4" sat_key="58760802" owner="20"
                sat_name="NCBI" owner_name="NCBI-Genomes" defdiv="GNM" length="620" extfeatmask="41"
            />
        </DocumentSummary>

    </DocumentSummarySet>
</eSummaryResult>
efetch.fcgi?db=<database>&id=<uid_list>&rettype=<retrieval_type>
&retmode=<retrieval_mode>
esearch.fcgi?db=<database>&term=<query>&usehistory=y

# esearch produces WebEnv value ($web1) and QueryKey value ($key1)

efetch.fcgi?db=<database>&query_key=$key1&WebEnv=$web1&rettype=
<retrieval_type>&retmode=<retrieval_mode>
elink.fcgi?dbfrom=<source_db>&db=<destination_db>&id=<uid_list>
elink.fcgi?dbfrom=<source_db>&db=<destination_db>&id=<uid1>&id=
<uid2>&id=<uid3>...
esearch.fcgi?db=<source_db>&term=<query>&usehistory=y

# esearch produces WebEnv value ($web1) and QueryKey value ($key1)

elink.fcgi?dbfrom=<source_db>&db=<destination_db>&query_key=
$key1&WebEnv=$web1&cmd=neighbor_history
elink.fcgi?dbfrom=<source_db>&db=<source_db>&id=<uid_list>&term=
<query>&cmd=neighbor_history
einfo.fcgi?db=<database>
<?xml version="1.0"?>
<!DOCTYPE eInfoResult PUBLIC "-//NLM//DTD eInfoResult, 11 May 2002//EN" 
"https://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd">
<eInfoResult>
<DbInfo>
<DbName>protein</DbName>
<MenuName>Protein</MenuName>
<Description>Protein sequence record</Description>
<Count>26715092</Count>
<LastUpdate>2009/05/12 04:39</LastUpdate>
<FieldList>
<Field>
<Name>ALL</Name>
<FullName>All Fields</FullName>
<Description>All terms from all searchable fields</Description>
<TermCount>133639432</TermCount>
<IsDate>N</IsDate>
<IsNumerical>N</IsNumerical>
<SingleToken>N</SingleToken>
<Hierarchy>N</Hierarchy>
<IsHidden>N</IsHidden>
</Field>
...
<Field>
<Name>PORG</Name>
<FullName>Primary Organism</FullName>
<Description>Scientific and common names 
of primary organism, and all higher levels of taxonomy</Description>
<TermCount>673555</TermCount>
<IsDate>N</IsDate>
<IsNumerical>N</IsNumerical>
<SingleToken>Y</SingleToken>
<Hierarchy>Y</Hierarchy>
<IsHidden>N</IsHidden>
</Field>
</FieldList>
<LinkList>
<Link>
<Name>protein_biosystems</Name>
<Menu>BioSystem Links</Menu>
<Description>BioSystems</Description>
<DbTo>biosystems</DbTo>
</Link>
...
<Link>
<Name>protein_unigene</Name>
<Menu>UniGene Links</Menu>
<Description>Related UniGene records</Description>
<DbTo>unigene</DbTo>
</Link>
</LinkList>
</DbInfo>
</eInfoResult>
egquery.fcgi?term=<query>
<?xml version="1.0"?>
<!DOCTYPE Result PUBLIC "-//NLM//DTD eSearchResult, January 2004//EN"
 "https://www.ncbi.nlm.nih.gov/entrez/query/DTD/egquery.dtd">
<!--
        $Id: egquery_template.xml 106311 2007-06-26 14:46:31Z osipov $
-->
<!-- ================================================================= -->
<Result>
        <Term>mouse[orgn]</Term>
        <eGQueryResult>
             <ResultItem>
                  <DbName>pubmed</DbName>
                  <MenuName>PubMed</MenuName>
                  <Count>0</Count>
                  <Status>Term or Database is not found</Status>
             </ResultItem>
             <ResultItem>
                  <DbName>pmc</DbName>
                  <MenuName>PMC</MenuName>
                  <Count>3823</Count>
                  <Status>Ok</Status>
             </ResultItem>
...
             <ResultItem>
                  <DbName>nuccore</DbName>
                  <MenuName>Nucleotide</MenuName>
                  <Count>1739903</Count>
                  <Status>Ok</Status>
             </ResultItem>
             <ResultItem>
                  <DbName>nucgss</DbName>
                  <MenuName>GSS</MenuName>
                  <Count>2264567</Count>
                  <Status>Ok</Status>
             </ResultItem>
             <ResultItem>
                  <DbName>nucest</DbName>
                  <MenuName>EST</MenuName>
                  <Count>4852140</Count>
                  <Status>Ok</Status>
             </ResultItem>
             <ResultItem>
                  <DbName>protein</DbName>
                  <MenuName>Protein</MenuName>
                  <Count>255212</Count>
                  <Status>Ok</Status>
             </ResultItem>
...
             <ResultItem>
                  <DbName>proteinclusters</DbName>
                  <MenuName>Protein Clusters</MenuName>
                  <Count>13</Count>
                  <Status>Ok</Status>
             </ResultItem>
        </eGQueryResult>
</Result>
espell.fcgi?term=<query>&db=<database>
<?xml version="1.0"?>
<!DOCTYPE eSpellResult PUBLIC "-//NLM//DTD eSpellResult, 23 November 
2004//EN" "https://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSpell.dtd">
<eSpellResult>
<Database>pmc</Database>
<Query>fiberblast cell grwth</Query>
<CorrectedQuery>fibroblast cell growth</CorrectedQuery>
<SpelledQuery>
 <Replaced>fibroblast</Replaced>
 <Original> cell </Original>
 <Replaced>growth</Replaced>
</SpelledQuery>
<ERROR/>
</eSpellResult>
#!/usr/local/bin/perl -w
# =======================================================================
#
#                            PUBLIC DOMAIN NOTICE
#               National Center for Biotechnology Information
#
#  This software/database is a "United States Government Work" under the
#  terms of the United States Copyright Act.  It was written as part of
#  the author's official duties as a United States Government employee and
#  thus cannot be copyrighted.  This software/database is freely available
#  to the public for use. The National Library of Medicine and the U.S.
#  Government have not placed any restriction on its use or reproduction.
#
#  Although all reasonable efforts have been taken to ensure the accuracy
#  and reliability of the software and data, the NLM and the U.S.
#  Government do not and cannot warrant the performance or results that
#  may be obtained by using this software or data. The NLM and the U.S.
#  Government disclaim all warranties, express or implied, including
#  warranties of performance, merchantability or fitness for any particular
#  purpose.
#
#  Please cite the author in any work or product based on this material.
#
# =======================================================================
#
# Author:  Oleg Khovayko
#
# File Description: eSearch/eFetch calling example
#  
# ---------------------------------------------------------------------
# Subroutine to prompt user for variables in the next section

sub ask_user {
  print "$_[0] [$_[1]]: ";
  my $rc = <>;
  chomp $rc;
  if($rc eq "") { $rc = $_[1]; }
  return $rc;
}

# ---------------------------------------------------------------------
# Define library for the 'get' function used in the next section.
# $utils contains route for the utilities.
# $db, $query, and $report may be supplied by the user when prompted; 
# if not answered, default values, will be assigned as shown below.

use LWP::Simple;

my $utils = "https://www.ncbi.nlm.nih.gov/entrez/eutils";

my $db     = ask_user("Database", "Pubmed");
my $query  = ask_user("Query",    "zanzibar");
my $report = ask_user("Report",   "abstract");

# ---------------------------------------------------------------------
# $esearch cont?ins the PATH & parameters for the ESearch call
# $esearch_result containts the result of the ESearch call
# the results are displayed ?nd parsed into variables 
# $Count, $QueryKey, and $WebEnv for later use and then displayed.

my $esearch = "$utils/esearch.fcgi?" .
              "db=$db&retmax=1&usehistory=y&term=";

my $esearch_result = get($esearch . $query);

print "\nESEARCH RESULT: $esearch_result\n";

$esearch_result =~ 
  m|<Count>(\d+)</Count>.*<QueryKey>(\d+)</QueryKey>.*<WebEnv>(\S+)</WebEnv>|s;

my $Count    = $1;
my $QueryKey = $2;
my $WebEnv   = $3;

print "Count = $Count; QueryKey = $QueryKey; WebEnv = $WebEnv\n";

# ---------------------------------------------------------------------
# this area defines a loop which will display $retmax citation results from 
# Efetch each time the the Enter Key is pressed, after a prompt.

my $retstart;
my $retmax=3;

for($retstart = 0; $retstart < $Count; $retstart += $retmax) {
  my $efetch = "$utils/efetch.fcgi?" .
               "rettype=$report&retmode=text&retstart=$retstart&retmax=$retmax&" .
               "db=$db&query_key=$QueryKey&WebEnv=$WebEnv";

  print "\nEF_QUERY=$efetch\n";     

  my $efetch_result = get($efetch);

  print "---------\nEFETCH RESULT(". 
         ($retstart + 1) . ".." . ($retstart + $retmax) . "): ".
        "[$efetch_result]\n-----PRESS ENTER!!!-------\n";
  <>;
}
#!/usr/local/bin/perl -w
# =======================================================================
#
#                            PUBLIC DOMAIN NOTICE
#               National Center for Biotechnology Information
#
#  This software/database is a "United States Government Work" under the
#  terms of the United States Copyright Act.  It was written as part of
#  the author's official duties as a United States Government employee and
#  thus cannot be copyrighted.  This software/database is freely available
#  to the public for use. The National Library of Medicine and the U.S.
#  Government have not placed any restriction on its use or reproduction.
#
#  Although all reasonable efforts have been taken to ensure the accuracy
#  and reliability of the software and data, the NLM and the U.S.
#  Government do not and cannot warrant the performance or results that
#  may be obtained by using this software or data. The NLM and the U.S.
#  Government disclaim all warranties, express or implied, including
#  warranties of performance, merchantability or fitness for any particular
#  purpose.
#
#  Please cite the author in any work or product based on this material.
#
# =======================================================================
#
# Author:  Oleg Khovayko
#
# File Description: ePost/eSummary calling example
#  

# ---------------------------------------------------------------------
my $eutils_root  = "https://www.ncbi.nlm.nih.gov/entrez/eutils";
my $ePost_url    = "$eutils_root/epost.fcgi";
my $eSummary_url = "$eutils_root/esummary.fcgi";

my $db_name = "PubMed";

# ---------------------------------------------------------------------
use strict;

use LWP::UserAgent;
use LWP::Simple;
use HTTP::Request;
use HTTP::Headers;
use CGI;

# ---------------------------------------------------------------------
# Read input file into variable $file
# File name - forst argument $ARGV[0]

undef $/;  #for load whole file

open IF, $ARGV[0] || die "Can't open for read: $!\n";
my $file = <IF>;
close IF;
print "Loaded file: [$file]\n";

# Prepare file - substitute all separators to comma

$file =~ s/\s+/,/gs;
print "Prepared file: [$file]\n";

#Create CGI param line

my $form_data = "db=$db_name&id=$file";

# ---------------------------------------------------------------------
# Create HTTP request

my $headers = new HTTP::Headers(
	Accept		=> "text/html, text/plain",
	Content_Type	=> "application/x-www-form-urlencoded"
);

my $request = new HTTP::Request("POST", $ePost_url, $headers );

$request->content($form_data);

# Create the user agent object

my $ua = new LWP::UserAgent;
$ua->agent("ePost/example");

# ---------------------------------------------------------------------
# send file to ePost by HTTP

my $response = $ua->request($request);

# ---------------------------------------------------------------------

print "Responce status message: [" . $response->message . "]\n";
print "Responce content: [" .        $response->content . "]\n";

# ---------------------------------------------------------------------
# Parse response->content and extract QueryKey & WebEnv
$response->content =~ 
  m|<QueryKey>(\d+)</QueryKey>.*<WebEnv>(\S+)</WebEnv>|s;

my $QueryKey = $1;
my $WebEnv   = $2;

print "\nEXTRACTED:\nQueryKey = $QueryKey;\nWebEnv = $WebEnv\n\n";

# ---------------------------------------------------------------------
# Retrieve DocSum from eSummary by simple::get method and print it
#
print "eSummary result: [" . 
  get("$eSummary_url?db=$db_name&query_key=$QueryKey&WebEnv=$WebEnv") . 
  "]\n";

Bookshelf

Entrez Programming Utilities Help [Internet].

E-utilities Quick Start

Authors

Affiliations

Release Notes

Announcement

Introduction

Searching a Database

Basic Searching

Storing Search Results

Associating Search Results with Existing Search Results

For More Information

Sample ESearch Output

Searching PubMed with Citation Data

Uploading UIDs to Entrez

Basic Uploading

Associating a Set of UIDs with Previously Posted Sets

For More Information

Sample EPost Output

Downloading Document Summaries

Basic Downloading

Downloading Data From a Previous Search

Sample ESummary Output

Sample ESummary version 2.0 Output

Downloading Full Records

Basic Downloading

Downloading Data From a Previous Search

Downloading a Large Set of Records

For More Information

Finding Related Data Through Entrez Links

Basic Linking

Batch mode – finds only one set of linked UIDs

‘By Id’ mode – finds one set of linked UIDs for each input UID

Finding Links to Data from a Previous Search

Finding Computational Neighbors Limited by an Entrez Search

For More Information

Getting Database Statistics and Search Fields

For More Information

Sample EInfo Output

Performing a Global Entrez Search

For More Information

Sample EGQuery Output

Retrieving Spelling Suggestions

For More Information

Sample ESpell Output

Demonstration Programs

EBot

Sample Perl Scripts

For More Information

Announcement Mailing List

Getting Help

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