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Entrez Programming Utilities
Updated:  August 9, 2004

Entrez Programming Utilities are tools that provide access to Entrez data outside of the regular web query interface and may be helpful for retrieving search results for future use in another environment.


User Requirements
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:

Database primary IDs:
Entrez Database Primary ID E-Utility Database Name
3D Domains 3D SDI domains
Domains PSSM-ID cdd
Genome Genome ID genome
Nucleotide GI number nucleotide
OMIM MIM number omim
PopSet Popset ID popset
Protein GI number protein
ProbeSet GEO ID geo
PubMed PMID pubmed
Structure MMDB ID structure
SNP SNP ID snp
Taxonomy TAXID taxonomy
UniGene UniGene ID unigene
UniSTS UniSTS ID unists

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=

Demonstration Programs
In order to demonstrate the capabilities of the E-Utilities (ESearch, EFetch and EPost, ESummary), NCBI has written two Perl scripts which may be downloaded and run from your machine.   Perl must be installed on your computer in order to run these programs, e.g., perl eutils_example.pl. After running the programs, we would recommend that you modify and extend them as you see fit to further examine the capabilities of the E-Utilities, to examine different databases, etc. Contained in the Perl script are comments describing the program design.

Click ESearch, EFetch or EPost, ESummary to retrieve the demonstration programs.  Select Save As from your web browser's File menu to save the programs on your computer. Internet Explorer users should choose Text File under Save as type.

Announcement Mailing List
For general announcements regarding the Entrez Utilities you may subscribe to the utilities-announce announcement mailing list. Please disregard the notice you receive about posting messages to the list. This mailing list is an announcement list only; individual subscribers may not send mail to this mailing list.  The list of subscribers is private.  You may subscribe on the web at:
http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce

Write to the Help Desk
Suggestions, comments, and questions specifically relating to the EUtility programs may be sent to eutilities@ncbi.nlm.nih.gov. Assistance with search queries and database content or corrections should be sent to the Help Desk

 
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