Add examples for Cat-VRS data classes

[DanielPuthawala]

It was expressed at the last Cat-VRS call that having examples alongside the schemata and docs really helped people new to the project to orient themselves. It was requested that we add additional examples (2 or 3 per class?) that demosntrate different aspects of the schemas.

[brendanreardon]

A non-exhaustive list of example updates that we want to make:

• Create a DefiningLocation constraint example that starts and ends with ranges, per Bob Dolin's recommendation
• Add HGVS mappings for all relevant examples
• Add an example that uses DefiningLocationConstraint with anyOf

[brendanreardon]

I just noticed that this thread may be a duplicate of #25. Should we close this in favor of the earlier one from Kori?

[korikuzma]

I can close mine!

[brendanreardon]

I committed hgvs representations to proteinSequenceConsequence-ex1.yaml. Some questions and comments that I have about the examples are...

• What do people think about not using the shorthand of vrs.json#ga4gh:VA.... for DefiningAlleleConstraint and members? I understand that this is quicker, but since it requires vrs-python to be set up locally to get unhash the id, it may add to confusion as new implementers are trying to get initiated.
• In the hgvs list extension for canonicalAllele-ex1.yaml, the first nucleotideExpression has "top-level" for the nucleotideType. What does this mean? I couldn't find anything about this in either the va-spec, vrs, or gks documentation either.
• As an aside, even though the extension field is unstructured, it may be nice to have documentation of why the examples are structured as they are. Regardless of how much documentation is written, in practice the examples are going to serve as templates for the community.
• All current examples using either DefiningAlleleConstraint or DefiningLocationConstraint list relations within the constraint. As a mappable concept, they should list more than just the primaryCode. Similar to above, it would be nice to have definitions for the primaryCodes being used in the current examples.
• Since the examples are written in .yaml, how do people feel about adding comments within the files? Specifically to link to relevant documentation for each section of an example. Alternatively, if folks are worried about cluttering the examples, we can add a README.md (or .rst) to the examples folder.

[jsstevenson]

What do people think about not using the shorthand of vrs.json#ga4gh:VA.... for DefiningAlleleConstraint and members? I understand that this is quicker, but since it requires vrs-python to be set up locally to get unhash the id, it may add to confusion as new implementers are trying to get initiated.

We really should have a simple web app for this (generating variation object/hash)