Tools/EndUserClients

Version 2 (modified by kono, 8 years ago)

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End-User Clients

BioMart

Cytoscape

Current Status

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

G-language

Galaxy

InterMine


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