Tools

Creating generic-yet-usable end user tools that work directly with the RDF graph data model.

Open Bio*

• Common API
  • User-side APIs
  • DB-side APIs (for triple store, Linked Data on the web)

• Programs
  • Data format converters
  • Tools for import/export/search

• Projects
  • BioRuby
  • BioPython?
  • BioPerl?
  • BioJava?
  • BioLib?

Text mining

• GO PubMed?
  • NER for genes, diseases, drugs
• MEDIE
• Query builder from natural language

Storage

• Existing triple stores
  • Virtuoso
  • ORACLE
  • :

• Evaluation
  • Scale?
  • Speed
  • Interface

End-user software

• Cytoscape
• BioMart?
• InterMine?
• Galaxy
• G-language