= 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
  * [http://search.cpan.org/~easr/ONTO-PERL-1.13/ 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 [http://couchdb.apache.org/ CoarchDB], [http://www.mongodb.org/ mongoDB] etc.)
  * biological:
    * Bio DB entries -> RDF (in [http://bioruby.org BioRuby] for [http://togows.dbcls.jp TogoWS], for example)
    * OBO <-> RDF (used in [http://cellcycleontology.org 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 [http://usegalaxy.org 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