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

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

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URL parameters:

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

• 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

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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

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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]

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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 parameterusehistory=y is included in an ESearch URL both a WebEnv (cookie string) andquery_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.

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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

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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=[e-mail]

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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|

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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

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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

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Retrieval Mode

Output format

Current values:

• xml
• html
• text
• asn.1

Example:

retmode=text

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Retrieval Type:

output types based on database

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

 

Sequence Options:

rettypescoperetmodeCommentxmltexthtml^*asn1native (full record)all but genexxxxDefault report for viewing sequencesfastasequence onlyxxxn/aFASTA view of a sequence. Existence of the mode depends on gi typegbnucleotide sequence onlyn/axxn/aGenBank report for sequences, constructed sequences will be shown as contigs (by pointing to its parts)gpprotein sequence onlyn/axxn/aGenPept reportgbwithpartsnucleotide sequence onlyn/axxn/aGenBank report for sequences, the sequence will always be showngbcnucleotide sequence onlyn/axxn/aINSDSeq structured flat filegpcprotein sequence onlyn/axxn/aINSDSeq structured flat fileestdbEST sequence onlyn/axxn/aEST ReportgssdbGSS sequence onlyn/axxn/aGSS Reportseqidsequence onlyn/axxn/aTo convert list of gis into list of seqidsaccsequence onlyn/axxxTo convert list of gis into list of accessionsftsequence onlyn/axxn/aFeature 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:

rettypeDescriptionschrSNP Chromosome reportfltSNP Flat File reportrsrSNP RS Cluster reportbriefSNP ID listdocsetSNP RS summary

Example:

rettype=fasta

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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