1. Tools
    1. Open Bio*
    2. Text mining
    3. End-user software
    4. Tutorial
    5. Basic Libraries

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

End-user software

  • Cytoscape
    • RDFScape Plugin
    • BioPAX Reader
  • BioMart
  • InterMine
  • Galaxy
  • G-language

Tutorial

* SparqlTutorial

Development plan and idea for end-user clients

Basic Libraries