Creating a Web Link to the Entrez Databases
Last Updated: October 13, 2004

• User System Requirements
• URL Parameters
  • Unique Identifiers
  • Database
  • Command
    • Search

      • Examples

      • Remove Filters
    • Date Ranging
      • Fixed Dates
      • Relative Dates
    • Retrieve
    • Link
    • Text
  • Format
  • Display Number
  • Tool
• Entrez Programming Utilities
• Leasing Data from the National Library of Medicine

User System Requirements
You may generate a query on your Web page and submit it to PubMed and the other Entrez databases providing that proper attribution is given to the US National Library of Medicine (NLM) and PubMed.  It must be clear to users that the search is actually being conducted at NLM. When you link to PubMed, present PubMed in a separate browser window that partially overlays your page. 

Do not overload NCBI's systems. Users intending to send numerous queries and/or retrieve large numbers of records from Entrez should comply with the following:

• Run retrieval scripts on weekends or between 9 PM and 5 AM ET weekdays for any series of more than 100 requests.
• Make no more than one request every 3 seconds.
• NCBI's Disclaimer and Copyright notice must be evident to users of your service. NLM does not claim the copyright on the abstracts in PubMed; however, journal publishers or authors may. NLM provides no legal advice concerning distribution of copyrighted materials, consult your legal counsel.

URL Parameters

Base URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?

Note: Do not use the PubMed URL alias, pubmed.gov, in constructing URL links to PubMed.

Unique Identifiers

Genome	Genome ID
Nucleotide	GI number
OMIM	MIM number
PopSet	GI number
Protein	GI number
PubMed	PMID
Structure	MMDB ID
Taxonomy	TAXID

Database

db=Entrez database name

Command

cmd=command

• Search - search terms with or without Boolean operators or search field qualifier tags
• Retrieve -  retrieve results in HTML format using unique identifiers
• Text  - retrieve results in text format using unique identifiers
• Link -  links to and displays the related results of the retrieved items using unique identifiers

Search
Include search terms with or without Boolean operators. Spaces within a URL should be "escaped" by converting them to '+' signs, e.g., Biochem Soc Trans should be entered as Biochem+Soc+Trans.

term=search terms

PubMed:
Search PubMed for citations about hay fever published in 2003:
cmd=search&db=pubmed&term=hay+fever+AND+2003[pdat]

Search PubMed for citations about arthritis and limit to the Complementary Medicine subset:
cmd=search&db=pubmed&orig_db=PubMed&term=arthritis&cmd_current=Limits
&pmfilter_Subsets=Complementary+Medicine

To turn off the filters use PubMedFilters=true:
cmd=search&term=hay+fever&db=pubmed&orig_db=pubmed&pubmedfilters=true

Search PubMed for citations on (hay fever OR asthma) AND (diet therapy OR drug therapy) and display the first 50 citations in citation format:
cmd=search&db=pubmed&term=(hay+fever+OR+asthma)+AND+(diet+therapy+OR+drug+therapy)
&dispmax=50&doptcmdl=citation 

Search PubMed for Provider Links for the text word p21:
cmd=search&db=pubmed&term=p21[tw]+AND+human[mh]&doptcmdl=externallink

See the PubMed Help to qualify search terms by search field tags.

Sequence Database:
Search the Protein database for AAC72193[accn] and display the results in GenPept format:
cmd=search&db=protein&term=AAC72193[accn]&doptcmdl=GenPept

Search Nucleotides for COMT sequences and display the brief format:
cmd=search&db=nucleotide&term=COMT&doptcmdl=Brief

See the Entrez Help to qualify search terms by search field tags.

OMIM:
Search OMIM for the FBN1 gene and display the Detailed format:
cmd=Search&db=omim&term=fbn1[gene]&doptcmdl=Detailed

See the OMIM Help to qualify search terms by search field tags.

Remove Filters

To turn off previously set filters use &db=database&orig_db=database&databasefilters=true

Where database is the Entrez database name, e.g.,

cmd=search&term=cat&db=nucleotide&orig_db=nucleotide&nucleotidefilters=true

Date Ranging
Not all dates are supported in all databases.  Date ranging can be fixed or relative.

Fixed Dates
Limit a search between two dates. Date parameters may be case sensitive, therefore use the exact value listed below.

• pmfilter_DateRange_Field=type+date, where type is one of the following:
• publication (PubMed, Protein and Nucleotide)
• entrez (PubMed)
• modification (Protein and Nucleotide)
• orig_db=database, where database is the same as db=
• filters=on
• pmfilter_DateRange_MinYear=yyyy
• pmfilter_DateRange_MinMonth=mm
• pmfilter_DateRange_MinDay=dd
• pmfilter_DateRange_MaxYear=yyyy
• pmfilter_DateRange_MaxMonth=mm
• pmfilter_DateRange_MaxDay=dd

Search PubMed for citations on hay fever from 1995/02/05 to 2003 enter:
cmd=search&term=hay+fever&db=pubmed&orig_db=pubmed&filters=on
&pmfilter_DateRange_Field=Publication+Date&pmfilter_DateRange_MinYear=1995
&pmfilter_DateRange_MinMonth=02&pmfilter_DateRange_MinDay=05&pmfilter_DateRange_MaxYear=2003

Relative Dates
Limit a search for citations where the date is between a number of days ago and today's date.

• pmfilter_XDatLimit=NNN+[Days/Years], where X is one of the following (X is case sensitive):
• E - Entrez (PubMed)
• P - Date of Publication (PubMed)
• M - Modification (Protein and Nucleotide)
• orig_db=database, where database is the same as db=

Search for PubMed citations on hay fever published within the last 90 days
cmd=search&term=hay+fever&db=PubMed&orig_db=pubmed&filters=on&pmfilter_EDatLimit=90+Days

Retrieve
Retrieve results in HTML using the unique identifier. Accession numbers cannot be retrieved via cmd=retrieve, use cmd=search.

list_uids=id,id,id

Retrieve PMIDs 10480954 and 12345 in the abstract format:
cmd=retrieve&db=pubmed&list_uids=10480954,12345&dopt=abstract

Link
Link to and display the related results of the retrieved items using the unique identifier. Accession numbers are not unique identifiers and cannot be retrieved with cmd=Link.

dbFrom=database searched (URL parameter is case sensitive)
db=database to retrieve links
from_uid=id

Retrieve Related Article links from PubMed PMID 10495220:
cmd=link&db=pubmed&dbFrom=pubmed&from_uid=10495220

Retrieve Nucleotide links from PubMed PMID 10492167:
cmd=link&db=nucleotide&dbFrom=pubmed&from_uid=10492167

Retrieve PubMed links from Nucleotide GI 4759059:
cmd=link&db=pubmed&dbFrom=nucleotide&from_uid=4759059

Text
Use Text to retrieve results in text format using the unique identifier.  Accession numbers are not unique identifiers and cannot be retrieved with cmd=Text.

uid=id&uid=id

Retrieve PubMed UIs 10480954, 10903209 in Text/Abstract format:
cmd=text&db=pubmed&uid=10903209&uid=10480954&dopt=Abstract

Retrieve Protein sequence records in flat file format for GIs 9367031, 729567, 586553
cmd=text&db=protein&dopt=genpept&dispmax=20&uid=9367031&uid=729567&uid=586553

Format

doptcmdl=format (use with cmd=search)
dopt=format  (use with cmd=retrieve and cmd=text)

Note: Scripts/programs that import XML should use E-Utilities.
 

Database	Report Format
PubMed	DocSum, Brief, Abstract, Citation, MEDLINE, XML, ASN1, ExternalLink
Nucleotide	DocSum, Brief, GenBank, ASN1, FASTA, ExternalLink, XML
OMIM	DocSum, Detailed, Synopsis, Variants,  MiniMIM, ASN1, ExternalLink
Protein	DocSum, Brief, GenPept, ASN1, FASTA, ExternalLink, XML
Genome	DocSum, Brief, ASN1, ExternalLink
Structure	DocSum, Brief
PopSet	DocSum, Brief, ASN1, FASTA, ExternalLink
Taxonomy	DocSum, Brief, TxUidList, TxInfo, TxTree, ExternalLink

Online help is available for the PubMed, Entrez, and OMIM format descriptions.

Display Number
Change the default number of items (20) displayed.

dispmax=number of items

Tool is a string with no internal spaces that identifies the resource that is using Entrez links. 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 the 'Tool' argument.

tool=resource name