turtle output format option does not have effect

[mhsano]

Using the -f turtle output option does not change the output format compared to the standard n-triples otutput. Maybe the turtle writer constructor needs to be parametrized with prefix/URI hashes (e.g. belv,...). Also standard prefixes should be written.

[abargnesi]

How are you running BEL to RDF conversion?

When running the commands you can do either of the following:

# (Recommended) Use the bel command with a bel2rdf subcommand.
bel bel2rdf --bel small_corpus.bel --format turtle

# (Deprecated) Use the bel2rdf.rb command.
bel2rdf.rb --bel small_corpus.bel --format turtle

There is a soft dependency on the rdf-turtle gem. You will receive an error, if this gem is not installed, with instructions on how to install it.

[mhsano]

I checked it. The output is in turtle format and the formatting option is correctly recognized.
However - the turtle output produced has only full URIs and no prefixes (e.g. belv:..., rdfs:....,). This limits readability.

It would help if the turtle writer would be parametrized with the standard RDF and OpenBEL prefix/URI combinations.

[abargnesi]

On the docket for 0.3.4. Work should include feature plus refactoring:

• Define comprehensive RDF and BEL prefixes for turtle output. ntriple/nquad formats will be unaffected since they do not support prefixes.
• Support reading / writing of supported RDF formats within the RDF Format extension and bel translate command.
• Allow options to be passed to Format extensions. Pass on through from bel translate.

[abargnesi]

bel.rb uses ruby-rdf/rdf for RDF capabilities. This gem includes well-known RDF vocabularies as Ruby constants. It would be wise to reuse these definitions and for BEL-specific vocabularies create our own vocabulary with ruby-rdf/rdf.

FYI as part of rdf 2.0.0 they have moved the vocabularies to a separate gem. Stick with using version 1.99.1 of the rdf gem.

At a later we can migrate to rdf 2.0.0.

[abargnesi]

The bel_schema.rb file in the rdf translator plugin declares some BEL-specific vocabularies for use with the rdf gem:

BELR    = ::RDF::Vocabulary.new('http://www.openbel.org/bel/')
BELV    = ::RDF::Vocabulary.new('http://www.openbel.org/vocabulary/')
BELE    = ::RDF::Vocabulary.new('http://www.openbel.org/evidence/')
PUBMED  = ::RDF::Vocabulary.new('http://bio2rdf.org/pubmed:')