= 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 || language || generic || [http://4store.org/trac/wiki/ClientLibraries 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