Version 6 (modified by ktym, 13 years ago)


Open Bio* Semantic Web tools


(Please add your name!)

  • Toshiaki Katayama
  • Erick Antezana

RDF libraries in each language

(Please add other languages as well!)

Name of the available libraries:


  • RDF reader (in)
  • RDF generator (out)
language in out
Ruby ? ?
Python o ?
Perl o ?

Tools to manipulate RDF data

  • RDF grep
  • RDF diff
  • RDF sort
  • RDF uniq
  • RDF wc (triple count)
  • RDF cat (combine)
    • (most of) these commands will output RDF graph :)
    • "sort" before "diff" is better.
    • it would be great if "diff" can have an option to ignore "empty node" which can shift internal IDs even if the graphs are almost same.

RDF converters

  • general:
    • RDF --> JSON (for CoarchDB, mongoDB etc.)
  • biological:
    • Bio DB entries -> RDF (in BioRuby for TogoWS, for example)
    • OBO <-> RDF (used in Cell Cycle Ontology because ".obo" file format is easy to read for human)

Interface for SPARQL endpoint

Language availability

Ruby ?
Python o
Perl ?
Java o
R ?

DBI like interface to Query and obtain Result by SPARQL.

  • automatically map to the relevant language object
  • we can use SPARQL endpoint as a data source for  Galaxy, for example.
  • sometimes, results can be huge

Language availability

Ruby ?
Python o
Perl ?
Java o
R ?

Try "short read archive (metadata) SPARQL endpoint" which will be developed by the NextGenSeq? open space discussion group.

Galaxy integration

  • Plugin development
  • Documentation