Version 1 - End Game

[larrybabb]

DMWG Interpretation v1 End Game

TODO 1. SEPIO ontology finalization (Matt B/Chris/Tristan/Bradford/Larry) - next Mon/Tue

• OWL, Protege work (All) - next Mon/Tue
• re-work data/code changes into our examples/build process (Larry) - (depends on above)

TODO 2. ClinGen Interpretation JSON-LD context build/publish (Tristan) - (this/next)

• allele context embedded in interp context (v1 solution)
• published - available file

DONE 3. VCI Interpretation Transformation Tool (Chris)

• break out reusable library into github project w/ documentation (Chris-done)
• tool, doc for transforming VCI to ClinGen Std Format (Chris-done)

TODO 4. ClinVar Submitter Tool (Larry/Tristan/Nafisa) -

• unit testing - this/next week - mostly complete
• integration testing (comparing existing to real ClinVar submissions)
• acceptance testing with SHarrison/MDistefano/SDwight? - next week

TODO 5. WebSite documentation (short-term) (Primary agenda for next Tuesday)

• (All) read all existing content and come to meeting with ideas (All)
• Re-org sections, gap analysis on missing content - divide conquer content generation
  • terminology
  • examples
  • entities/types/concepts/resources?
• Re-org doc build for website without major overhaul (Nafisa, Tristan, Bradford) COMPLETE!

[bpow]

TODO 2 is issue #107 , and I think I may have satisfied it. The context is now being generated within the config.rb (so at middleman build time) from the data in data/flattened and is available at http://datamodel.clinicalgenome.org/interpretation/json/context

There is probably a better filename/path to use for this, so if someone has ideas they can update the relevant proxy statement in config.rb.

The context can still be generated from the external script construct_context.rb outside of the build process.

[cbizon]

What do you think of interpretation.jsonld?

[bpow]

The idiomatic way to make a json-ld context available seems to be to use a rather generic/top-levelish URL (like http://schema.org) with the context being served when there is a request header of Accept: application/ld+json.

However, I don't think that is possible with github pages.

I don't feel strongly about the filename of the context (since it has to be a file), happy to defer to consensus. Do we want to include the version in the filename (instead of just in the path)?

[larrybabb]

refactored in December.