Add resource API to access BEL SKOS vocabularies

[abargnesi]

This task would be to allow access to query BEL SKOS vocabularies such as Hgnc Human Genes, Ncbi Taxonomy, and Uberon.

Motivation / Use Cases

• Equivalence of namespace values, terms, statements, and evidence
  • Find all equivalences
  • Find target equivalence (i.e. in a specific concept scheme)
  • Normalization of identifiers (e.g. Hgnc Human Genes -> Entrez Gene, Mesh Processes -> Go Biological Process)
• Orthologization of namespace values, parameters, terms, and evidence
• With the inclusion of historical relations between SKOS concepts we could support
  • Upgrade namespace values, parameters, terms, and evidence
  • Validation

Approach

• Access RDF store through ruby-rdf/rdf using the repository abstraction. Initially provide a SPARQL client implementation.
• Implement resource API on the repository abstraction.
• Investigate plugging in Apache Jena as a ruby-rdf repository for efficient, in process access. This has it's benefits in terms of performance, but suffers from a single JVM locked against a TDB store.
• Create transform functions using the resource API to allow transformations of large collections of BEL evidence.

[abargnesi]

Limiting the scope of this based on needs. The following will be implemented:

• RDF Repository abstraction using RDF.rb. Implemented as plugins in bel.rb.
• APIs that enumerates/resolve resources and values using an RDF Repository.