PubMed

Nucleotide

Protein

Genome

NLM Catalog

OMIM

PMC

Taxonomy

SNP

Gene

NCBI Entrez Utilities Web Service

Updated: May 20, 2008

 

The NCBI Entrez Utilities Web Service enables developers to access Entrez Utilities via the Simple Object Access Protocol (SOAP).

The Web Service has been tested with:

• C# and Visual Basic in MS Visual Studio 2005
• Java (Apache Axis2 version 1.4)
• MS SOAP Toolkit 3.0 and MS Word Visual Basic

 

The Web Service also should work with the older versions of Axis (Axis for Java ver. 1.4) and MS Visual Studio (MSVS 2003).

Developers can also use other SOAP libraries and tools to access NCBI Entrez Utilities Web Service, but some features might be not working there.

Version 2.0 (current)

 

What's new in version 2.0

Version 2.0 provides access to EGQuery, ESummary, EInfo, ELink, ESearch, ESpell, EPost and EFetch utilities.

To create a SOAP client application developer should use one or more of the following WSDLs:

• http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/eutils.wsdl, which includes all utilities but EFetch.
• http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/eutils_MS.wsdl, which provides methods with a different input parameters style (old style).
• WSDL to fetch records from a corresponding database:

  o    Pubmed:	http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/efetch_pubmed.wsdl
  o    PMC:	http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/efetch_pmc.wsdl
  o    NlmCatalog:	http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/efetch_nlmc.wsdl
  o    Journals:	http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/efetch_journals.wsdl
  o    OMIM:	http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/efetch_omim.wsdl
  o    Taxonomy:	http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/efetch_taxon.wsdl
  o    SNP:	http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/efetch_snp.wsdl
  o    Gene:	http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/efetch_gene.wsdl
  o    Sequences :	http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/efetch_seq.wsdl
  Sequences are protein, nuccore, nucgss, nucest, genome, and popset databases.

The input parameters for the SOAP version of the Entrez Utilities are the same as described in the documentation for each individual utility except no retmode parameter is available as the SOAP implementation only returns XML.

Known issues

• Both Axis2 and MS Visual Studio 2005 fail to work with efetch_pmc.wsdl because it includes MathML schema which has a circular group references. The older versions, Axis 1.4 and MS Visual Studio 2003, work fine.
• eFetch utility generates an invalid XML for SNP, so currently it doesn't work through SOAP. The bug is being fixed.
• eutils_MS.wsdl defines message parts not quite correctly, so WSDL2Java utility from Axis2, which cares about binding style, fails to generate a Java code.
• WSDL2Java from Axis2 generates for efetch_gene.xsd a source code which could not be compiled.

How to Use E-Utilities Web Service

 

• with C# and MS Visual Studio 2005
• with VB and MS Visual Studio 2005
• with Java and Apache Axis2
• with MS SOAP Toolkit 3.0

 

See also:

 

• What is a Web Service?
• User System Requirements
• Entrez DTDs
• Announcement Mailing List
• Help Desk

 

Previous versions

Version 1.5

• SOAP implementation of E-Utilities
• Light version (no eFetch)
• eFetch only
• eFetch for PubMed and NlmCatalog

Version 1.4

• SOAP implementation of E-Utilities

Version 1.3

• SOAP implementation of E-Utilities

Version 1.2

• SOAP implementation of E-Utilities

Version 1.1

• SOAP implementation of E-Utilities

Version 1.0

• SOAP implementation for EFetch
• SOAP implementation for ESummary, ESearch, EInfo, ELink and EGQuery

 

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