|Version 6 (modified by ktym, 7 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:
- ActiveRDF: may depends on Rails
- RDF: generic RDF library
- ONTO-PERL: it might be used (it is, however, OBO-centric http://search.cpan.org/~easr/ONTO-PERL-1.13/)
- RDF reader (in)
- RDF generator (out)
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 --> JSON (for CoarchDB, mongoDB etc.)
- 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
Try "short read archive (metadata) SPARQL endpoint" which will be developed by the NextGenSeq? open space discussion group.
- Plugin development