Open Bio* Semantic Web tools

Participants

(Please add your name!)

• Toshiaki Katayama
• Erick Antezana

RDF libraries in each language

(Please add other languages as well!)

Name of the available libraries:

• Ruby
  • ActiveRDF: may depends on Rails
• Python
  • librdf
• Perl
  • RDF: generic RDF library
  • ONTO-PERL: it might be used (it is, however, OBO-centric  http://search.cpan.org/~easr/ONTO-PERL-1.13/)

 http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn042

Functionality

• 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