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Untitled

I'm really frustrated by the quality of the documentation here http://www.ncbi.nlm.nih.gov/entrez/query/enwiki/static/eutils_help.html Specifically I'd like to find a table of allowed retmode and rettype values broken down by database. I'm sure there was a table like this somewhere on the help page, but I can't find it. --Dan|^(talk) 17:51, 28 January 2009 (UTC)[reply]

eUtils

I found the following information on eUtils invaluable (but hidden) [1]. I'll try to pear it down and add it to the article at some point. --Dan|^(talk) 09:05, 29 January 2009 (UTC)[reply]

EFetch for Sequence and other Molecular Biology Databases

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
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 (db)

db=

Current database values:

gene
genome
nucleotide
nuccore
nucest
nucgss
protein
popset
snp
sequences (composite name, including nucleotide, protein, popset and genome)

Web Environment

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

WebEnv=WgHmIcDG], etc.

Query_key

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

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.

tool=

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.

email=

Sequence Databases

You got to love this document.

Record Identifier

IDs required if WebEnv is not used.

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

Current values:

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

Display Numbers

retstart=x (x= sequential number of the first id retrieved - default=0 which will retrieve the first record)

retmax=y (y= number of items retrieved)

Parameters specific to sequence databases

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

Retrieval Mode

retmode=output format

Current values:

xml
html
text
asn.1

Retrieval Type

rettype=output types based on database

Current values and descriptions: Type descriptions:

rettype	scope	Descriptions
native (full record)	all but Gene	Default format for viewing sequences.
fasta	sequence only	FASTA view of a sequence.
gb	nucleotide sequence only	GenBank view for sequences, constructed sequences will be shown as contigs (by pointing to its parts).
gbc	nucleotide sequence only	INSDSeq structured flat file.
gbwithparts	nucleotide sequence only	GenBank view for sequences, the sequence will always be shown.
est	dbEST sequence only	EST Report.
gss	dbGSS sequence only	GSS Report
gp	protein sequence only	GenPept view
gpc	protein sequence only	INSDSeq structured flat file.
seqid	sequence only	To convert list of gis into list of seqids.
acc	sequence only	To convert list of gis into list of accessions
chr	dbSNP only	SNP Chromosome Report.
flt	dbSNP only	SNP Flat File report.
rsr	dbSNP only	SNP RS Cluster report.
brief	dbSNP only	SNP ID list.
docset	dbSNP only	SNP RS summary.

Not all Retrieval Modes are possible with all Retrieval Types.

Sequence Options

	native	fasta	gb	gbwithparts	est	gss	gp	seqid	acc	gbc	gpc
xml	x	x*	n/a	n/a	TBI	TBI	n/a	TBI	TBI	x	x
text	x	x	x*	x*	x*	x*	x*	x	x	n/a	n/a
html	x	x	x*	x*	x*	x*	x*	x	x	n/a	n/a
asn.1	x	n/a	n/a	n/a	n/a	n/a	n/a	x	n/a	n/a	n/a