EFetch for Sequence and other Molecular Biology Databases

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)
• Record Identifiers (id)
• Tool (tool)
• E-mail address (email)
• Display Numbers (retstart, retmax)
• Report formats and specifiers (rettype, retmode):
  • Retrieval Type and Mode for sequence databases
  • Retrieval Type and Mode for genome databases
  • Retrieval Type and Mode for SNP database
  • Retrieval Type and Mode for SRA database

Database

Current database values:

1. gene
2. snp
3. popset
4. sequences:
   • genome
   • nucleotide:
     • nuccore
     • nucest
     • nucgss
   • protein
5. sra

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=NCID_1_23402205_210.26.30.681_3051_6265373359

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.

Record Identifier

IDs required if WebEnv is not used.

Current values:

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

Example:

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

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

Example:

email=john@doe.org

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

Retrieval Type and Mode

x – retrieval mode available. Click to it to run an example
^*  – the same content as text report but with some HTML elements (anchors, sections, etc)
n/a – not available

Example:

rettype=gb&retmode=text