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