Entrez | PubMed | Nucleotide | Protein | Genome | Structure | OMIM | PMC | Journals | Books |
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.
Additional information is available in the NCBI Bookshelf Short Courses Building Customized Data Pipelines Using the Entrez Programming Utilities (eUtils) and the NCBI PowerScripting course.
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:
EInfo lists all E-Utility database names. Primary IDs, which are always an integer, are listed below for a few databases:
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 that 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
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 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 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 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
Please see the
PubMed or Entrez help for assistance with search queries and database content.
Suggestions, comments, and questions specifically relating to the EUtility programs may be sent to eutilities@ncbi.nlm.nih.gov.