oba: ontology based answers

The oba project provides a service to facilitate the access to ontologies for applications and workflows. The service maps the content of ontologies to an object oriented model and makes i accessible through the network as RESTful service. In addition the oba service can be used to answer ontological questions, such as to which organ an arbitrary anatomical entity belongs.

Publication:
Dönitz, J. and Wingender, E.:
The ontology-based answers (OBA) service: A connector for embedded usage of ontologies in applications
Front. Gene. 3, 197 (2012). link

Documentation

The interface of the oba service is free to be used for the implementation of own clients or embedding into workflows. As an example for the usage, an open source Java connector, which utilizes the Cytomer ontology, is provided for download (see below). Additionally to the example client, which can be used for demostration and testing, a generic client is provided for download, which you can extend for your own purposes.

The interface of the oba service is documented in a manual, which is also available from this page. In the manual you will find a detailed description of the syntax, and the input and return values of the functions.

The client can be downloaded and embedded into Java applications by adding the jar file to the classpath. By default the client will connect to the public oba-server. If the Cytomer connector is run from a command line (java -jar cytomer-*.jar) a simple test client is run, which calls some functions of the public server and prints the results to the console

Parts of the oba-service

oba-client.zip

The zip file contains the basic client and the Cytomer client as single jar file containing all dependencies.

oba-server.zip

If required, the server can be downloaded and run locally. The zip file for the server contains also the Cytomer ontologie, the Tribolium ontology and plugins with semantic functions. The jar file "oba-server-*.jar can be run from the command line or using the start script on Linux and MacOS. After startup the oba-server is available at port 9998.

Downloads

OBA-client

OBA-server

Reference projects

The oba service is used in the following applications and projects: