R K B

The RKB ontology forms part of the Semantic Science projects. The RDF/OWL files containing only the terminology of our latest version RKB v0.2 can be downloaded from its Google Code page found here.

We have also made available for download a version of RKB v0.2 with loaded individuals for all 7 models of the NMR structure for PDB:1AM0, an RNA Aptamer complex, which can be downloaded here.

1. To enable the viewing of the RKB you will need to have installed an OWL editor. We recommend the usage of Protege 4, which can be downloaded from here. Choose the appropiate platform, download and install.
2. Launch Protege 4 and load the RKB. On the welcome screen select "Open Ontology from URI" and copy into the URI text-box one of the following URIs:
   • (A) http://semanticscience.googlecode.com/svn/tags/RKB-0.2/rna-with-individuals.owl
   • (B) http://semanticscience.googlecode.com/svn/tags/RKB-0.2/rna.owl
   
   (A) Contains individuals for all models of PDB:1AM0 and (B) has only the terminology for RKB with no individuals.
3. Once the ontology has loaded, you may want to change the way that class names are rendered. To do so in Protege simply go to File->Preferences and in the Renderer tab select "Render entities using annotation values", then click on the "Annotations..." button to specify which annotations to use for class names then select the "Add annotations" button and select the IAO_0000111, click "Ok". Now the classnames should be displayed by the value contained in the IAO label.
4. Try our sample queries found in the documentation section.