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

•  Raptor RDF Parser Library
  •  rapper − Raptor RDF parsing and serializing utility
•  Rasqal RDF Query Library
•  pellet owl reasoning and data validation