The WSDbfetch service allows you to retrieve entries from various up-to-date biological databases using entry identifiers or accession numbers. This is equivalent to the CGI based dbfetch service.

WSDbfetch currently supports the following databases:

• Nucleotide sequences: embl emblann emblcds emblcon emblsva refseq
• Protein sequences: uniprotkb uniref100 uniref50 uniref90 uniparc unisave refseqp
• Protein structures: pdb
• Patented protein sequences: epo_prt uspto_prt jpo_prt
• Literature: medline
• Specialized: genomereviews hgvbase interpro ipi

Data can be retrieved in range of formats.

For more information see:

• The dbfetch service

For details of the service used by these clients see WSDbfetch Web Service.

The Microsoft .NET runtime is already installed on most MS Windows systems. The Microsoft .NET runtime is available via Microsoft Update or as a download (see http://msdn.microsoft.com/netframework/).

For MacOS X, Linux and other non-Windows systems see Mono or DotGNU.

Download the C# client:

• Executable: wsdbfetch.exe
• Source code: wsdbfetch.cs

Run without arguments to get a usage summary:

wsdbfetch.exe

Download and unzip the library files lib-1.4.zip and add the jars to the Java classpath.

Download the Java client:

• Executable: WSDbfetch.jar
• Source code: WSDbfetchClient.java

To get usage information run the client without arguments:

java -Djava.ext.dirs=lib -jar WSDbfetch.jar

To run the Perl client you need to install SOAP::Lite. SOAP::Lite is a collection of Perl modules which provides a simple and lightweight interface to SOAP both on client and server side. This client requires SOAP::Lite version 0.60.

Download the Perl client: dbfetch.pl

To get usage information run without arguments:

perl dbfetch.pl

A number of example clients are available in a range of languages:

• PHP (tutorial)
  • nuSOAP: wsdbfetch_cli_nusoap.php
  • PEAR SOAP: wsdbfetch_cli_pear_soap.php
  • PHP SOAP: wsdbfetch_cli_php_soap.php5
• Python (tutorial)
  • Using SOAPpy: wsdbfetch.py
  • Using ZSI: wsdbfetch_zsi.py
• Ruby (tutorial)
  • Using SOAP4r: wsdbfetch.rb
• Visual Basic .NET (tutorial)
  • Executable: wsdbfetch.exe
  • Source: wsdbfetch.vb

Workflow engines such as Taverna and Triana offer a simple way of combining individual web services into complex applications.

A basic workflow showing how to use WSDbfetch can be found on myExperiment.