OpenTox Ontology service

The Ontology service is an implementation of OpenTox Ontology service API.

OpenTox Ontology service.

The Ontology Service does not depend on AMBIT modules, and compiles into a different web application. It currently uses the Jena TDB persistence mechanism, and was initially designed as a proof-of-concept service to illustrate the added value of gathering RDF triples of several remote OpenTox services into the same triple storage and enabling SPARQL queries.

Please note: AMBIT REST web services do not require an Ontology service to be installed. However, some applications like ToxPredict and Bioclipse-OpenTox depend on querying an OpenTox Ontology service.

Currently, the Ontology service is used as a registry of all deployed OpenTox services (both local and remote), and ToxPredict web application retrieves the list of QSAR models via SPARQL query.

Download OpenTox Ontology service v.0.0.2

Web application archive
ontology.war

Deployment

  1. Copy ontology.war under webapps directory of the servlet container. The application should be accessible at
     http://localhost:8080/ontology

Configuration

Does not use MySQL database. Uses Jena TDB for persistent storage (file based), which is automatically generated on deploy. The following configuration files can be found under webapps/ontology folder. There are reasonable default values.

WEB-INF/classes/org/opentox/config/config.properties

#tdb or sdb , currently tdb supported only 
persistence=${jena.persistence}
#where to store TDB files. Default is java temporary directory
tdb=THE-PATH-TO-THE-TDB-FOLDER

WEB-INF/classes/org/opentox/config/aa.properties 

aa.opensso=URI-OF-OPENTOX-OPENSSO-SERVICE
aa.policy=URI-OF-OPENTOX-POLICY-SERVICE

Models registration

        curl -X POST -d "uri=THE-URI" http://yourhost:8080/ontology -H "subjectid:OPENSSOTOKEN"

Or use the HTML form at the top, paste the URI of the model and click "Submit".

Publication

Jeliazkova 2010
Jeliazkova N., Jeliazkov V. AMBIT RESTful web services: an implementation of the OpenTox application programming interface, Journal of Cheminformatics 2011, 3:18, doi:10.1186/1758-2946-3-18.

The code

v.0.0.2
https://ambit.svn.sourceforge.net/svnroot/ambit/tags/ontology-service-0.0.2
current development
https://ambit.svn.sourceforge.net/svnroot/ambit/branches/opentox/ontology-service

Maven artifact

Artifact

<dependency>
  <groupId>org.opentox</groupId>
  <artifactId>ontology</artifactId>
  <version>0.0.2</version>
  <type>war</type>
</dependency>

Repository

   <repository>
        <id>ambit-plovdiv-releases</id>
        <url>http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/releases</url>
    </repository>