| | 2 | |
| | 3 | == !BioMart == |
| | 4 | |
| | 5 | == Cytoscape == |
| | 6 | |
| | 7 | === Current Status === |
| | 8 | Cytoscape already has some tools related to semantic web technology: |
| | 9 | * [http://www.bioinformatics.org/rdfscape/wiki/Main/HomePage RDFScape Plugin] - Plugin supports for reasoning on ontologies. Also supports query/result visualization. |
| | 10 | * BioPAX Reader - simply read and convert basic information stored in BioPAX level 2. |
| | 11 | And there are some issues: |
| | 12 | * RDFScape is a bit hard to use for average users (biologists). Need to refactor user interface. |
| | 13 | * Typing SPARQL query is powerful for hardcore users, but too difficult for biologists. |
| | 14 | * After Cytoscape reads BioPAX data, no semantics are used. |
| | 15 | |
| | 16 | === Potential Projects for Hackathon === |
| | 17 | * Re-design RDFScape UI |
| | 18 | * User-friendly Query Builder |
| | 19 | * Automatic data import - load selected set of ontologies automatically |
| | 20 | * Internal data management - how should Cytoscape store semantics from BioPAX data files? |
| | 21 | * Merge networks/attributes automatically using semantics |
| | 22 | |
| | 23 | == G-language == |
| | 24 | |
| | 25 | == Galaxy == |
| | 26 | |
| | 27 | == !InterMine == |
| | 28 | |
| | 29 | |
| | 30 | ---- |
| | 31 | |
| | 32 | [wiki:Tools Back to Tools page] |
