Open Bio* Semantic Web tools

Participants

(Please add your name!)

• Toshiaki Katayama
• Erick Antezana
• Shuichi Kawashima

RDF libraries in each language

(Please add other languages as well!)

Name of the available libraries:

• Ruby
  • ActiveRDF: may depends on Rails
  • We have a lot more. see -->  http://raa.ruby-lang.org/search.rhtml?search=rdf
• Python
  • librdf
• Perl
  • RDF: generic RDF library
  •  ONTO-PERL: it might be used (it is, however, OBO-centric  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

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

language	generic	4store
Ruby	o	o
Python	o	o
Perl	?	x
Java	o	o
R	?	?

• 4store
  • database server  http://4store.org/
    • install doc in Japanese  http://lifesciencedb.g.hatena.ne.jp/nakao_mitsuteru/20100105/1262713627
    • binary download for mac  http://dl.dropbox.com/u/152468/4store-1.0.2.dmg
  • client library for Ruby/Python/Java  http://4store.org/trac/wiki/ClientLibraries
• Virtuoso
  • database server  http://virtuoso.openlinksw.com/dataspace/dav/wiki/Main/ ->  http://sourceforge.net/projects/virtuoso/files/

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

Galaxy integration

• Plugin development
• Documentation