Web Service

We provide java code download for PINA web service query client. As the PINA web service complies with the latest specifications of RESTful web service, there is no restriction on the programming language of the client implementation.


  • Aug 2, 2011: Change from SOPA to RESTful web service. It is easier to run now, no need to install Axis2 library anymore.
  • July 27, 2010: PINA can be accessed by the PINA component in the Anduril framework microarray bundle.
  • Nov 27, 2008: Java query client is updated to support reading input from a file and writeing output to a file.
  • July 28, 2008: Web service supports returning query result in GraphML format now. Query client is also updated, but previous client is also compatible with the upgraded service and can still work.

2.Client Install

  1. Download PINA-WSclient_02082011.zip and unarchive the file.
  2. Other requirements: JRE 6 or above and Apache Ant 1.5 or above are needed.


  1. Modify values in the build.properties file (instructions included as comments in the file);
  2. Check the example file PINAClient.java under the directory src and modify it as you like.

4. Compile and Run

  1. Type ant run in the command line within the installation directory of this program.

5. URL documentation

For other programming language users, the simplicity of RESTful web service is to allow you fetching the content using the URL described below. The structure of the URL to fetch data from PINA RESTful web service is as:
e.g. http://omics.bjcancer.org:80/pina/restWS/current/getInteractors/Q96KC2,Q9P2D1?format=mitab
The URL consists of five parts:


The first part of the URL is the location of PINA RESTful web service: http://cbg.garvan.unsw.edu.au/pina/restWS


Currently only one version of PINA RESTful web service exist. More versions may exist in the future. The current version will be the symbolic link of the last version of PINA web service.


Methods Description
getInteractors To search interactors of query proteins.
getInteractions To check whether pairs of proteins can find interactions in PINA. For example,


When searching interactors, the query must be one or more UniPort ACs separated by commas.

When searching protein pairs, the query must be one or more pairs of UniProt ACs. Within each pair, UniProt ACs must be separated by underscore; while multiple pairs must be separated by commas.


Parameter name Parameter values
format sif (Cytoscape)
mitab (PSI-MITAB 2.5)
graphml (GraphML)

5.6 Examples

Fetch interacting proteins of ARL5B(Q96KC2) and KIAA1416(Q9P2D1):

Check whether there are interactions among three pairs of proteins: