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  • Configuring annotations and namespaces in bel.rb (2016-01-21)
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Description

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.

Attendees

Discussion

  1. BEL URIs are not linked and are not common (e.g. identifiers.org/…).

  2. 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).

  3. Follow up with closed issue #40 to see if chemical terms are handled. Add test if not present.

  4. BEL scripts with custom, non-openbel namespaces do not result in a URI when converting to RDF.

Proposal:

Allow annotation and namespace overrides when translating to RDF. Opened issue #92 with more detail.