Cytoscape already has some tools related to semantic web technology:
- RDFScape Plugin - Plugin supports for reasoning on ontologies. Also supports query/result visualization.
- BioPAX Reader - simply read and convert basic information stored in BioPAX level 2.
And there are some issues:
- RDFScape is a bit hard to use for average users (biologists). Need to refactor user interface.
- Typing SPARQL query is powerful for hardcore users, but too difficult for biologists.
- After Cytoscape reads BioPAX data, no semantics are used.
Potential Projects for Hackathon
- Re-design RDFScape UI
- User-friendly Query Builder
- Automatic data import - load selected set of ontologies automatically
- Internal data management - how should Cytoscape store semantics from BioPAX data files?
- Merge networks/attributes automatically using semantics