NCBI Entrez Utilities Web Service

Updated: April 17, 2009

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 2005/2008
Java (Apache Axis2 version 1.4.1)
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)

Date: 17/04/2009

efetch_gene.xsd and efetch_seq.xsd have been updated to support latest changes in DTD.
Please update your C#/Java projects and rebuild your applications if you use efetch_gene.wsdl or efetch_seq.wsdl.

Date: 12/29/2009

efetch_pubmed.xsd has been updated to support the new PubMed 2009 DTD.
Please update your C#/Java projects and rebuild your applications if you use efetch_pubmed.wsdl.

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. This can be fixed if you add some prefix to local variables names in Value_type47 declaration. For example, add "x" as a prefix, so _fun variable become x_fun and fun variable become xfun, etc. There 34 variable names to change: _fun, _inv, _mam, _org, _phg, _pln, _pri, _pro, _rod, _syn, _una, _vrl, _vrt, _pat, _est, _sts, _other, fun, inv, mam, org, phg, pln, pri, pro, rod, syn, una, vrl, vrt, pat, est, sts, other.

How to Use E-Utilities Web Service

Previous versions

Version 1.5

NCBI Entrez Utilities Web Service

Version 2.0 (current)

Known issues

How to Use E-Utilities Web Service

See also:

Previous versions

Version 1.5

Version 1.4

Version 1.3

Version 1.2

Version 1.1

Version 1.0