Version 0.5.0

Fixes

Fix missing RDF prefixes when converting BEL Script to RDF (Issue #71)

There was an issue where the RDF prefix would not serialize to RDF using either bel translate bel rdf or bel2rdf.rb.
The issue was diagnosed, by @sanea, to be an issue with parsing BEL Script files in chunks. The missing prefix would always occur between the chunks of the file. More details in PR #99.

Error translating to JSON Evidence format using Oj adapter (Issue #93)

Writing JSON Evidence to a string was not supported within the translator when using the Oj adapter to serialize JSON. Now a StringIO is constructed to allow returning a JSON string.

Consistent representation of Annotation and Namespace references in Evidence model and translators (Issue #94)

The translator plugins did not agree on the format of annotation and namespace references. All have been updated to read/write annotations and namespaces as arrays of hashes. This schema further describes the format from the JSON Evidence perspective.

RDF conversion of Parameter does not include encoding type statement (Issue #96)

The encoding type of BEL parameters were not converted to RDF statements. The following example shows a BEL term that includes the encoding type of its BEL parameter:

<ns1:Term rdf:about='http://www.openbel.org/bel/p_HGNC_KRAS'>
    <rdf:type rdf:resource='http://www.openbel.org/vocabulary/ProteinAbundance'></rdf:type>
    <ns0:label>p(HGNC:KRAS)</ns0:label>
    <ns3:hasConcept>
      <ns5:AbundanceConcept rdf:about='http://www.openbel.org/bel/namespace/hgnc-human-genes/KRAS'>
        <rdf:type rdf:resource='http://www.openbel.org/vocabulary/GeneConcept'></rdf:type>
        <rdf:type rdf:resource='http://www.openbel.org/vocabulary/RNAConcept'></rdf:type>
        <rdf:type rdf:resource='http://www.openbel.org/vocabulary/ProteinConcept'></rdf:type>
      </ns5:AbundanceConcept>
    </ns3:hasConcept>
  </ns1:Term>

Additions

• Introduced translators for additional RDF formats; split and removed the RDF translator in favor of one translator per RDF format (Issue #95).
• Warn when BEL namespace data could not be retrieved (Issue #97).
• Added generator for random BEL Nanopubs using the bel generate subcommand (Issue #102).
• Access BEL annotation resource values from external .belanno files (Issue #100).
• Support different types of serialization within the BEL Script translator (Issue #98).