EFetch for Sequence and other Molecular Biology Databases (please see http://eutils.ncbi.nlm.nih.gov

Last updated: $Date: 2009-03-23 18:22:05 -0400 (Mon, 23 Mar 2009) $

EFetch documenation is also available for the Literature, and Taxonomy databases.

EFetch: Retrieves records in the requested format from a list of one or more unique identifiers.

• URL Parameters
• Examples
• User System Requirements
• Entrez DTDs
• Demonstration Program
• Announcement Mailing List

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

URL parameters:

NOTE: Utility parameters may be case sensitive. Use lower case characters for all parameters except WebEnv

• Database (db)
• Web Environment (WebEnv)
• Query key (query_key)
• Tool (tool)
• E-mail address (email)
• Record identifier (id)
• Display Numbers (retstart retmax)
• Parameters specific to sequence databases
• Retrieval mode or output format
• Retrieval type

Database

Current database values:

• gene
• genome
• nucleotide:
  • nuccore
  • nucest
  • nucgss
• protein
• popset
• snp
• sequences - Composite name including nucleotide, protein, popset and genome

Example:

db=protein

Web Environment (WebEnv)

History link value previously returned in XML results from ESearch and used with EFetch in place of primary ID result list.

Example:

WebEnv=WgHmIcDG]

Query Key

The value used for a history search number or previously returned in XML results from Esearch or EPost.

Example:

query_key=6

Note: WebEnv is similar to the cookie that is set on a user's computers when accessing PubMed on the web.  If the parameter usehistory=y is included in an ESearch URL both a WebEnv (cookie string) and query_key (history number) values will be returned in the results. Rather then using the retrieved PMIDs in an ESummary URL you may simply use the WebEnv and query_key values to retrieve the records. WebEnv will change for each ESearch query.

Tool

A string with no internal spaces that identifies the resource which is using Entrez links (e.g., tool=flybase). This argument is used to help NCBI provide better service to third parties generating Entrez queries from programs. As with any query system, it is sometimes possible to ask the same question different ways, with different effects on performance. NCBI requests that developers sending batch requests include a constant 'tool' argument for all requests using the utilities.

Example:

tool=flybase

E-mail Address

If you choose to provide an email address, we will use it to contact you if there are problems with your queries or if we are changing software interfaces that might specifically affect your requests. If you choose not to include an email address we cannot provide specific help to you,  but you can still sign up for utilities-announce to receive general

announcements.

Example:

[email protected]

Record Identifier

IDs required if WebEnv is not used.

Current values:

• NCBI sequence number (GI)
• accession
• accession.version
• fasta
• GeneID
• genome ID
• seqid

Example:

id=123,U12345,U12345.1,gb|U12345|

Display Numbers

• retstart - sequential number of the first id retrieved - default=0 which will retrieve the first record
• retmax - number of items retrieved

Example:

retstart=100&retmax=50

Sequence Strand, Start, Stop and Complexity Parameters

• strand - what strand of DNA to show (1 = plus or 2 = minus)
• seq_start - show sequence starting from this base number
• seq_stop - show sequence ending on this base number
• complexity - gi is often a part of a biological blob, containing other gis

  Complexity regulates the display:

  • 0 - get the whole blob
  • 1 - get the bioseq for gi of interest (default in Entrez)
  • 2 - get the minimal bioseq-set containing the gi of interest
  • 3 - get the minimal nuc-prot containing the gi of interest
  • 4 - get the minimal pub-set containing the gi of interest

Example:

strand=2&seq_start=50&seq_stop=2000&complexity=2

Retrieval Mode

Output format

Current values:

• xml
• html
• text
• asn.1

Example:

retmode=text

Retrieval Type:

output types based on database

Note: Not all Retrieval Modes are possible with all Retrieval Types.

 

Sequence Options:

rettype	scope	retmode				Comment
		xml	text	html*	asn1
native (full record)	all but gene	x	x	x	x	Default report for viewing sequences
fasta	sequence only	x	x	x	n/a	FASTA view of a sequence. Existence of the mode depends on gi type
gb	nucleotide sequence only	n/a	x	x	n/a	GenBank report for sequences, constructed sequences will be shown as contigs (by pointing to its parts)
gp	protein sequence only	n/a	x	x	n/a	GenPept report
gbwithparts	nucleotide sequence only	n/a	x	x	n/a	GenBank report for sequences, the sequence will always be shown
gbc	nucleotide sequence only	n/a	x	x	n/a	INSDSeq structured flat file
gpc	protein sequence only	n/a	x	x	n/a	INSDSeq structured flat file
est	dbEST sequence only	n/a	x	x	n/a	EST Report
gss	dbGSS sequence only	n/a	x	x	n/a	GSS Report
seqid	sequence only	n/a	x	x	n/a	To convert list of gis into list of seqids
acc	sequence only	n/a	x	x	x	To convert list of gis into list of accessions
ft	sequence only	n/a	x	x	n/a	Feature Table report

x – retrieval mode available. Click to it to run an example
^*  – the same content as text report but with some HTML links
n/a – not available

SNP options:

rettype	Descriptions
chr	SNP Chromosome report
flt	SNP Flat File report
rsr	SNP RS Cluster report
brief	SNP ID list
docset	SNP RS summary

Example:

rettype=fasta

Examples

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

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=5&complexity=0&rettype=fasta

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=5&rettype=gb&seq_start=1&seq_stop=9

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.cgi?db=nucleotide&id=5&rettype=fasta&seq_start=1&seq_stop=9&strand=2

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

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

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

Entrez display format GBSeqXML:

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

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

Entrez display format TinySeqXML:

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

Entrez Gene, full display as xml:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2&retmode=xml