RDFScape is a plugin that has been developed to extend a software oriented to biological analysis with support for reasoning on ontologies in the semantic web framework. We show with this plugin how the use of ontological knowledge in biological analysis can be extended through the use of inference. In particular, we present two examples relative to ontologies representing biological pathways: we demonstrate how these can be abstracted and visualized as interaction networks, and how reasoning on causal dependencies within elements of pathways can be implemented.
A core component of RDFScape was re-engineered in 2008 for continuing ‘Affymetrix’ analyses. This component allows the definition of functions based on ontology patterns, and their computation on numeric values. It is intended in particular to be used to define pathway scoring functions, based on microarray data, that will include causal and functional information found in pathway ontologies.
This project is relevant also for the Pathway based analysis and it now attributes an increased value to pathway-based information. For these reasons, we have chosen to provide this module as independent from RDFScape.
We will explore the possibilities offered by RDFScape and the related function evaluator on pathways curated within DC-THERA and the database provided by Duccio Cavalieri.