We have a question about one of the open issues in GitHub: OpenBEL/bel.rb#65 - about changing URIs in bel2rdf to follow identifiers.org conventions. First of all, since this impacts more than just bel2rdf (it also impacts the resource-generator and so on), I think it would be useful for us to get together with you briefly to make sure that we coordinate - perhaps, rather than just modifying bel2rdf, or modifying the resource-generator, it would be better to encapsulate the URI generation somehow, so it can be used by multiple other modules.
BEL URIs are not linked and are not common (e.g. identifiers.org/…).
Custom namespaces used: MicroRNA namespaces (mirbase), enzymes, groups, and complexes (some have names). List of compound names are defined as a custom namespace. Chemical structures are defined in a separate file using inchi format (see ChemSpider RDF for ideas).
Follow up with closed issue #40 to see if chemical terms are handled. Add test if not present.
BEL scripts with custom, non-openbel namespaces do not result in a URI when converting to RDF.
Allow annotation and namespace overrides when translating to RDF. Opened issue #92 with more detail.