Web services: Java library

We provide a library for convenient communication, within a Java program, with the Systems Biology Ontology's web services.


This describes the new version of the libary (using a new web services stack, JAX-WS). For more information, you can have a look at the what's new? section of the documentation.

Download

Two versions of the library are provided (distributed under the terms of the GNU Lesser General Public License) from the SourceForge project (latest release: 2.0.0).

Dependencies

In case you want to use the light version.

Tutorial

A full sample program showing the usage of the library is available for download.

The results obtained should be similar to these ones.

The Javadoc of this library is available here.

Here is an overview of the usage of the library and some useful methods provided:

    // creation of the link to the SBO Web Services
    SBOLink link = new SBOLink();
    
    // is your library the latest available?
    boolean libraryUpdated = link.isLibraryUpdated();
    
    // conversion of identifier (integer one into the official one)
    String id = link.convertId(192);   // should return 'SBO:0000192'
    
    // term retrieval (with direct access to its details)
    Term term = link.getTerm("SBO:0000192");
    String name = term.getName();
    String mathml = term.getMathml();
    
    // OWL retrieval
    String owl = link.getOWLTerm("SBO:0000144");
    
    // generic search
    List<Term> terms = link.search("Henri-Michaelis-Menten");
    
    // framework retrieval
    String frameworkId = link.getFramework("SBO:0000076");
    
    // parents retrieval
    List<String> parentIds = link.getParents("SBO:0000028");
    
    // and much more...