EMBL-EBI Web Services

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====== WSDbfetch (RPC/encoded SOAP) Clients ======

===== Description =====

The [[services:dbfetch|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 [[http://www.ebi.ac.uk/cgi-bin/dbfetch|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 [[http://www.ebi.ac.uk/cgi-bin/dbfetch|dbfetch]] service

===== Web Service =====

For details of the service used by these clients see [[services:dbfetch|WSDbfetch Web Service]].

===== C# .NET Client =====

=== .NET runtime ===

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 [[http://www.mono-project.com/|Mono]] or [[http://www.gnu.org/software/dotgnu/|DotGNU]].

=== Get the client ===

Download the C# client:
  * Executable: ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/csharp/bin/wsdbfetch.exe|wsdbfetch.exe]]''
  * Source code: ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/csharp/src/wsdbfetch.cs|wsdbfetch.cs]]''

Run without arguments to get a usage summary:
<code csh>wsdbfetch.exe</code> 
<BR>

===== Java Client =====

=== Dependencies ===

Download and unzip the library files ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/java/lib-1.4.zip|lib-1.4.zip]]'' and add the jars to the Java classpath.

=== Get the client ===

Download the Java client:
  * Executable: ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/java/bin/WSDbfetch.jar|WSDbfetch.jar]]''
  * Source code: ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/java/src/uk/ac/ebi/webservices/WSDbfetchClient.java|WSDbfetchClient.java]]''

To get usage information run the client without arguments:
<code>java -Djava.ext.dirs=lib -jar WSDbfetch.jar</code>
<BR>

===== Perl Client =====

=== Install SOAP::Lite ===

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  [[http://search.cpan.org/~byrne/SOAP-Lite-0.60a/|SOAP::Lite version 0.60]].

=== Get the client ===

Download the Perl client: ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/perl/soaplite/dbfetch.pl|dbfetch.pl]]''

To get usage information run without arguments:
<code csh>perl dbfetch.pl</code> 
<BR>
===== Other Clients =====

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

  * PHP ([[:tutorials:06_Programming:PHP|tutorial]])
    * nuSOAP: ''[[https://svn.ebi.ac.uk/webservices/webservices-1.0/trunk/clients/php/wsdbfetch_cli_nusoap.php|wsdbfetch_cli_nusoap.php]]''
    * PEAR SOAP: ''[[https://svn.ebi.ac.uk/webservices/webservices-1.0/trunk/clients/php/wsdbfetch_cli_pear_soap.php|wsdbfetch_cli_pear_soap.php]]''
    * PHP SOAP: ''[[https://svn.ebi.ac.uk/webservices/webservices-1.0/trunk/clients/php/wsdbfetch_cli_php_soap.php|wsdbfetch_cli_php_soap.php5]]''
  * Python ([[:tutorials:06_Programming:Python|tutorial]])
    * Using SOAPpy: ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/python/soappy_clients/wsdbfetch.py|wsdbfetch.py]]''
    * Using ZSI: ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/python/zsi_clients/wsdbfetch_zsi.py|wsdbfetch_zsi.py]]''
  * Ruby ([[:tutorials:06_Programming:Ruby|tutorial]])
    * Using SOAP4r: ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/ruby/wsdbfetch.rb|wsdbfetch.rb]]''
  * Visual Basic .NET ([[:tutorials::06_Programming:dot_net:vb.net|tutorial]])
    * Executable: ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/vb.net/wsdbfetch.exe|wsdbfetch.exe]]''
    * Source: ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/vb.net/wsdbfetch.vb|wsdbfetch.vb]]''

===== Workflows =====

Workflow engines such as [[http://taverna.sourceforge.net/|Taverna]] and [[http://www.trianacode.org/|Triana]] offer a simple way of combining individual web services into complex applications.

==== Taverna ====

A basic workflow showing how to use WSDbfetch can be found on [[http://www.myexperiment.org/workflows/209|myExperiment]].
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