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The E-utilities In-Depth: Parameters, Syntax and More

, PhD.

Created: ; Last Update: February 14, 2014.

Introduction

This chapter serves as a reference for all supported parameters for the E-utilities, along with accepted values and usage guidelines. This information is provided for each E-utility in sections below, and parameters and/or values specific to particular databases are discussed within each section. Most E-utilities have a set of parameters that are required for any call, in addition to several additional optional parameters that extend the tool's functionality. These two sets of parameters are discussed separately in each section.

General Usage Guidelines

Please see Chapter 2 for a detailed discussion of E-utility usage policy. The following two parameters should be included in all E-utility requests.

tool

Name of application making the E-utility call. Value must be a string with no internal spaces.

email

E-mail address of the E-utility user. Value must be a string with no internal spaces, and should be a valid e-mail address.

E-utility DTDs

With the exception of EFetch, the E-utilities each generate a single XML output format that conforms to a DTD specific for that utility. Please follow the links below to access the E-utility DTDs:

ESummary version 2.0 produces unique XML DocSums for each Entrez database, and as such each Entrez database has a unique DTD for version 2.0 DocSums. Links to these DTDs are provided in the version 2.0 XML.

EFetch produces output in a variety of formats, some of which are XML. Most of these XML formats also conform to DTDs or schema specific to the relevant Entrez database. Please follow the links below for PubMed DTDs:

EInfo

Base URL

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi

Functions

  • Provides a list of the names of all valid Entrez databases
  • Provides statistics for a single database, including lists of indexing fields and available link names

Required Parameters

None. If no db parameter is provided, einfo will return a list of the names of all valid Entrez databases.

Optional Parameters

db

Target database about which to gather statistics. Value must be a valid Entrez database name.

version

Used to specify version 2.0 EInfo XML. The only supported value is ‘2.0’. When present, EInfo will return XML that includes two new fields: <IsTruncatable> and <IsRangeable>. Fields that are truncatable allow the wildcard character ‘*’ in terms. The wildcard character will expand to match any set of characters up to a limit of 600 unique expansions. Fields that are rangeable allow the range operator ‘:’ to be placed between a lower and upper limit for the desired range (e.g. 2008:2010[pdat]).

retmode

Retrieval type. Determines the format of the returned output. The default value is ‘xml’ for EInfo XML, but ‘json’ is also supported to return output in JSON format.

Examples

Return a list of all Entrez database names:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi

Return version 2.0 statistics for Entrez Protein:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=protein&version=2.0

ESearch

Base URL

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi

Functions

  • Provides a list of UIDs matching a text query
  • Posts the results of a search on the History server
  • Downloads all UIDs from a dataset stored on the History server
  • Combines or limits UID datasets stored on the History server
  • Sorts sets of UIDs

Required Parameters

db

Database to search. Value must be a valid Entrez database name (default = pubmed).

term

Entrez text query. All special characters must be URL encoded. Spaces may be replaced by '+' signs. For very long queries (more than several hundred characters long), consider using an HTTP POST call. See the PubMed or Entrez help for information about search field descriptions and tags. Search fields and tags are database specific.

esearch.fcgi?db=pubmed&term=asthma

Optional Parameters – History Server

usehistory

When usehistory is set to 'y', ESearch will post the UIDs resulting from the search operation onto the History server so that they can be used directly in a subsequent E-utility call. Also, usehistory must be set to 'y' for ESearch to interpret query key values included in term or to accept a WebEnv as input.

WebEnv

Web environment string returned from a previous ESearch, EPost or ELink call. When provided, ESearch will post the results of the search operation to this pre-existing WebEnv, thereby appending the results to the existing environment. In addition, providing WebEnv allows query keys to be used in term so that previous search sets can be combined or limited. As described above, if WebEnv is used, usehistory must be set to 'y'.

esearch.fcgi?db=pubmed&term=asthma&WebEnv=<webenv string>&usehistory=y

query_key

Integer query key returned by a previous ESearch, EPost or ELink call. 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). For query_key to function, WebEnv must be assigned an existing WebEnv string and usehistory must be set to 'y'.

Values for query keys may also be provided in term if they are preceeded by a '#' (%23 in the URL). While only one query_key parameter can be provided to ESearch, any number of query keys can be combined in term. Also, if query keys are provided in term, they can be combined with OR or NOT in addition to AND.

The following two URLs are functionally equivalent:

esearch.fcgi?db=pubmed&term=asthma&query_key=1&WebEnv=
<webenv string>&usehistory=y

esearch.fcgi?db=pubmed&term=%231+AND+asthma&WebEnv=
<webenv string>&usehistory=y

Optional Parameters – Retrieval

retstart

Sequential index of the first UID in the retrieved set to be shown in the XML output (default=0, corresponding to the first record of the entire set). This parameter can be used in conjunction with retmax to download an arbitrary subset of UIDs retrieved from a search.

retmax

Total number of UIDs from the retrieved set to be shown in the XML output (default=20). By default, ESearch only includes the first 20 UIDs retrieved in the XML output. If usehistory is set to 'y', the remainder of the retrieved set will be stored on the History server; otherwise these UIDs are lost. Increasing retmax allows more of the retrieved UIDs to be included in the XML output, up to a maximum of 100,000 records. To retrieve more than 100,000 UIDs, submit multiple esearch requests while incrementing the value of retstart (see Application 3).

rettype

Retrieval type. There are two allowed values for ESearch: 'uilist' (default), which displays the standard XML output, and 'count', which displays only the <Count> tag.

retmode

Retrieval type. Determines the format of the returned output. The default value is ‘xml’ for ESearch XML, but ‘json’ is also supported to return output in JSON format.

sort

Specifies the method used to sort UIDs in the ESearch output. The available values vary by database (db) and may be found in the Display Settings menu on an Entrez search results page. If usehistory is set to ‘y’, the UIDs are loaded onto the History Server in the specified sort order and will be retrieved in that order by ESummary or EFetch. Example values are ‘relevance’ and ‘name’ for Gene and ‘first+author’ and ‘pub+date’ for PubMed. Users should be aware that the default value of sort varies from one database to another, and that the default value used by ESearch for a given database may differ from that used on NCBI web search pages.

field

Search field. If used, the entire search term will be limited to the specified Entrez field. The following two URLs are equivalent:

esearch.fcgi?db=pubmed&term=asthma&field=title

esearch.fcgi?db=pubmed&term=asthma[title]

Optional Parameters – Dates

datetype

Type of date used to limit a search. The allowed values vary between Entrez databases, but common values are 'mdat' (modification date), 'pdat' (publication date) and 'edat' (Entrez date). Generally an Entrez database will have only two allowed values for datetype.

reldate

When reldate is set to an integer n, the search returns only those items that have a date specified by datetype within the last n days.

mindate, maxdate

Date range used to limit a search result by the date specified by datetype. These two parameters (mindate, maxdate) must be used together to specify an arbitrary date range. The general date format is YYYY/MM/DD, and these variants are also allowed: YYYY, YYYY/MM.

Examples

Search in PubMed with the term cancer for abstracts that have an Entrez date within the last 60 days; retrieve the first 100 PMIDs and translations; post the results on the History server and return a WebEnv and query_key:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=cancer&reldate=60&datetype=edat&retmax=100&usehistory=y

Search in PubMed for the journal PNAS, Volume 97, and retrieve six PMIDs starting with the seventh PMID in the list:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=PNAS[ta]+AND+97[vi]&retstart=6&retmax=6&tool=biomed3

Search in the NLM Catalog for journals matching the term obstetrics:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nlmcatalog&term=obstetrics+AND+ncbijournals[filter]

Search PubMed Central for free full text articles containing the query stem cells:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pmc&term=stem+cells+AND+free+fulltext[filter]

Search in Nucleotide for all tRNAs:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleotide&term=biomol+trna[prop]

Search in Protein for a molecular weight range:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=protein&term=70000:90000[molecular+weight]

EPost

Base URL

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi

Functions

  • Uploads a list of UIDs to the Entrez History server
  • Appends a list of UIDs to an existing set of UID lists attached to a Web Environment

Required Parameters

db

Database containing the UIDs in the input list. The value must be a valid Entrez database name (default = pubmed).

id

UID list. Either a single UID or a comma-delimited list of UIDs may be provided. All of the UIDs must be from the database specified by db. There is no set maximum for the number of UIDs that can be passed to epost, but if more than about 200 UIDs are to be posted, the request should be made using the HTTP POST method.

epost.fcgi?db=protein&id=15718680,157427902,119703751

Optional Parameter

WebEnv

Web Environment. If provided, this parameter specifies the Web Environment that will receive the UID list sent by post. EPost will create a new query key associated with that Web Environment. Usually this WebEnv value is obtained from the output of a previous ESearch, EPost or ELink call. If no WebEnv parameter is provided, EPost will create a new Web Environment and post the UID list to query_key 1.

epost.fcgi?db=protein&id=15718680,157427902,119703751&WebEnv=
<webenv string>

ESummary

Base URL

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi

Functions

  • Returns document summaries (DocSums) for a list of input UIDs
  • Returns DocSums for a set of UIDs stored on the Entrez History server

Required Parameter

db

Database from which to retrieve DocSums. The value must be a valid Entrez database name (default = pubmed).

Required Parameter – Used only when input is from a UID list

id

UID list. Either a single UID or a comma-delimited list of UIDs may be provided. All of the UIDs must be from the database specified by db. There is no set maximum for the number of UIDs that can be passed to ESummary, but if more than about 200 UIDs are to be provided, the request should be made using the HTTP POST method.

esummary.fcgi?db=protein&id=15718680,157427902,119703751

Required Parameters – Used only when input is from the Entrez History server

query_key

Query key. This integer specifies which of the UID lists attached to the given Web Environment will be used as input to ESummary. Query keys are obtained from the output of previous ESearch, EPost or ELink calls. The query_key parameter must be used in conjunction with WebEnv.

WebEnv

Web Environment. This parameter specifies the Web Environment that contains the UID list to be provided as input to ESummary. Usually this WebEnv value is obtained from the output of a previous ESearch, EPost or ELink call. The WebEnv parameter must be used in conjunction with query_key.

esummary.fcgi?db=protein&query_key=<key>&WebEnv=<webenv string>

Optional Parameters – Retrieval

retstart

Sequential index of the first DocSum to be retrieved (default=1, corresponding to the first record of the entire set). This parameter can be used in conjunction with retmax to download an arbitrary subset of DocSums from the input set.

retmax

Total number of DocSums from the input set to be retrieved, up to a maximum of 10,000. If the total set is larger than this maximum, the value of retstart can be iterated while holding retmax constant, thereby downloading the entire set in batches of size retmax.

retmode

Retrieval type. Determines the format of the returned output. The default value is ‘xml’ for ESummary XML, but ‘json’ is also supported to return output in JSON format.

version

Used to specify version 2.0 ESummary XML. The only supported value is ‘2.0’. When present, ESummary will return version 2.0 DocSum XML that is unique to each Entrez database and that often contains more data than the default DocSum XML.

EFetch

Base URL

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi

Functions

  • Returns formatted data records for a list of input UIDs
  • Returns formatted data records for a set of UIDs stored on the Entrez History server

Required Parameters

db

Database from which to retrieve records. The value must be a valid Entrez database name (default = pubmed). Currently EFetch does not support all Entrez databases. Please see Table 1 in Chapter 2 for a list of available databases.

Required Parameter – Used only when input is from a UID list

id

UID list. Either a single UID or a comma-delimited list of UIDs may be provided. All of the UIDs must be from the database specified by db. There is no set maximum for the number of UIDs that can be passed to EFetch, but if more than about 200 UIDs are to be provided, the request should be made using the HTTP POST method.

efetch.fcgi?db=protein&id=15718680,157427902,119703751

Required Parameters – Used only when input is from the Entrez History server

query_key

Query key. This integer specifies which of the UID lists attached to the given Web Environment will be used as input to EFetch. Query keys are obtained from the output of previous ESearch, EPost or ELInk calls. The query_key parameter must be used in conjunction with WebEnv.

WebEnv

Web Environment. This parameter specifies the Web Environment that contains the UID list to be provided as input to EFetch. Usually this WebEnv value is obtained from the output of a previous ESearch, EPost or ELink call. The WebEnv parameter must be used in conjunction with query_key.

efetch.fcgi?db=protein&query_key=<key>&WebEnv=<webenv string>

Optional Parameters – Retrieval

retmode

Retrieval mode. This parameter specifies the data format of the records returned, such as plain text, HMTL or XML. See Table 1 for a full list of allowed values for each database.

Image

Table

Table 1 – Valid values of &retmode and &rettype for EFetch (null = empty string)

rettype

Retrieval type. This parameter specifies the record view returned, such as Abstract or MEDLINE from PubMed, or GenPept or FASTA from protein. Please see Table 1 for a full list of allowed values for each database.

retstart

Sequential index of the first record to be retrieved (default=0, corresponding to the first record of the entire set). This parameter can be used in conjunction with retmax to download an arbitrary subset of records from the input set.

retmax

Total number of records from the input set to be retrieved, up to a maximum of 10,000. Optionally, for a large set the value of retstart can be iterated while holding retmax constant, thereby downloading the entire set in batches of size retmax.

Optional Parameters – Sequence Databases

strand

Strand of DNA to retrieve. Available values are "1" for the plus strand and "2" for the minus strand.

seq_start

First sequence base to retrieve. The value should be the integer coordinate of the first desired base, with "1" representing the first base of the seqence.

seq_stop

Last sequence base to retrieve. The value should be the integer coordinate of the last desired base, with "1" representing the first base of the seqence.

complexity

Data content to return. Many sequence records are part of a larger data structure or "blob", and the complexity parameter determines how much of that blob to return. For example, an mRNA may be stored together with its protein product. The available values are as follows:

Value of complexityData returned for each requested GI
0entire blob
1bioseq
2minimal bioseq-set
3minimal nuc-prot
4minimal pub-set

Examples

PubMed

Fetch PMIDs 17284678 and 9997 as text abstracts:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=17284678,9997&retmode=text&rettype=abstract

Fetch PMIDs in XML:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11748933,11700088&retmode=xml

PubMed Central

Fetch XML for PubMed Central ID 212403:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=212403

Nucleotide/Nuccore

Fetch the first 100 bases of the plus strand of GI 21614549 in FASTA format:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=21614549&strand=1&seq_start=1&seq_stop=100&rettype=fasta&retmode=text

Fetch the first 100 bases of the minus strand of GI 21614549 in FASTA format:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=21614549&strand=2&seq_start=1&seq_stop=100&rettype=fasta&retmode=text

Fetch the nuc-prot object for GI 21614549:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=21614549&complexity=3

Fetch the full ASN.1 record for GI 5:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=5

Fetch FASTA for GI 5:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=5&rettype=fasta

Fetch the GenBank flat file for GI 5:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=5&rettype=gb

Fetch GBSeqXML for GI 5:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=5&rettype=gb&retmode=xml

Fetch TinySeqXML for GI 5:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=5&rettype=fasta&retmode=xml

Popset

Fetch the GenPept flat file for Popset ID 12829836:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=popset&id=12829836&rettype=gp

Protein

Fetch the GenPept flat file for GI 8:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=8&rettype=gp

Fetch GBSeqXML for GI 8:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=8&rettype=gp&retmode=xml

Sequences

Fetch FASTA for a transcript and its protein product (GIs 312836839 and 34577063)

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=sequences&id=312836839,34577063&rettype=fasta&retmode=text

Gene

Fetch full XML record for Gene ID 2:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2&retmode=xml

EGQuery

Base URL

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/egquery.fcgi

Function

Provides the number of records retrieved in all Entrez databases by a single text query.

Required Parameter

term

Entrez text query. All special characters must be URL encoded. Spaces may be replaced by '+' signs. For very long queries (more than several hundred characters long), consider using an HTTP POST call. See the PubMed or Entrez help for information about search field descriptions and tags. Search fields and tags are database specific.

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/egquery.fcgi?term=asthma

ESpell

Base URL

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/espell.fcgi

Function

Provides spelling suggestions for terms within a single text query in a given database.

Required Parameters

db

Database to search. Value must be a valid Entrez database name (default = pubmed).

term

Entrez text query. All special characters must be URL encoded. Spaces may be replaced by '+' signs. For very long queries (more than several hundred characters long), consider using an HTTP POST call. See the PubMed or Entrez help for information about search field descriptions and tags. Search fields and tags are database specific.

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/espell.fcgi?db=pubmed&term=asthmaa+OR+alergies

ECitMatch

Base URL

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/ecitmatch.cgi

Function

Retrieves PubMed IDs (PMIDs) that correspond to a set of input citation strings.

Required Parameters

db

Database to search. The only supported value is ‘pubmed’.

rettype

Retrieval type. The only supported value is ‘xml’.

bdata

Citation strings. Each input citation must be represented by a citation string in the following format:

journal_title|year|volume|first_page|author_name|your_key|

Multiple citation strings may be provided by separating the strings with a carriage return character (%0D). The your_key value is an arbitrary label provided by the user that may serve as a local identifier for the citation, and it will be included in the output. Be aware that all spaces must be replaced by ‘+’ symbols and that citation strings should end with a final vertical bar ‘|’.

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/ecitmatch.cgi?db=pubmed&retmode=xml&bdata=proc+natl+acad+sci+u+s+a|1991|88|3248|mann+bj|Art1|%0Dscience|1987|235|182|palmenberg+ac|Art2|

Release Notes

ESearch &sort; JSON output format: February 14, 2014

  • ESearch now provides a supported sort parameter
  • EInfo, ESearch and ESummary now provide output data in JSON format

ECitMatch, EInfo Version 2.0, EFetch: August 9, 2013

  • ECitMatch is a new E-utility that serves as an API to the PubMed batch citation matcher
  • EInfo has an updated XML output that includes two new fields: <IsTruncatable> and <IsRangeable>
  • EFetch now supports the BioProject database.

EFetch Version 2.0. Target release date: February 15, 2012

  • EFetch now supports the following databases: biosample, biosystems and sra
  • EFetch now has defined default values for &retmode and &rettype for all supported databases (please see Table 1 for all supported values of these parameters)
  • EFetch no longer supports &retmode=html; requests containing &retmode=html will return data using the default &retmode value for the specified database (&db)
  • EFetch requests including &rettype=docsum return XML data equivalent to ESummary output

Release of new Genome database: November 9, 2011

ESummary Version 2.0. November 4, 2011

  • ESummary now supports a new, alternative XML presentation for Entrez document summaries (DocSums). The new XML is unique to each Entrez database and generally contains more extensive data about the record than the original DocSum XML.
  • There are no plans at present to discontinue the original DocSum XML, so developers can continue to use this presentation, which will remain the default.
  • Version 2.0 XML is returned when &version=2.0 is included in the ESummary URL.

Demonstration Programs

Please see Chapter 1 for sample Perl scripts.

For More Information

Please see Chapter 1 for getting additional information about the E-utilities.

PubReader format: click here to try

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