GKS namespace questions

[larrybabb]

GKS VA-Spec, Cat-VRS and VRS all work together on a GKS-Core set of schemas.

Would we create a namespace for GKS, or would we create one for each product (including the shared one)? Is there going to be a "best practice" within GA4GH schema registry to define namespaces that make sense?

gks-core
vrs
cat-vrs
va-spec

are the 4 repos we have right now that each have their own schemas, some of which depend on others. VA-Spec is the most complex since it has sub-namespaces for community guidelines. And there's some degree of volatility around the fact that we may change the way we group or namespace things.

I think we would need to work with you guys to figure out how you envision all this working in the registry.

[ianfore]

@larrybabb that's the kind of question we need to explore.

For example gks-core has eight JSON schema - but in another sense there is one overall gks-core schema - expressed in .yml file. I don't think we should fall into the trap of thinking that schema means JSON schema.

And then you have the relationships between them.

I don't think the fact that the schemas needing to refer to one another is a reason in itself to put them in the same namespace. It seems pretty likely that some GA4GH system would need to use a schema from some other completely separate GA4GH system. And we need the volatility and to move things around as you suggest. Both those points seem to to suggest that references to other schema likely should include the namespace of the referent schema.

See the notebook here which implements the (evolving) Schema Registry spec against your GitHub repos for gks-core and vrs. It treated them as different namespaces - but that could be changed

Agree with your bottom line, and would suggest that using working examples is good way to figure it out.

[ianfore]

@larrybabb as you'd mentioned them above, I added cat-vrs and va-spec to the implementation. All of these were straightforward to do as you'd followed the same repo pattern with a folder with all the json schema in. Ping me via email and I can give you the URL that the implementation is running on.

va-spec was the slight exception in that you have four sub folders within the schema folder; aac-2017, acmg-2015, base and ccv-2022. For now I just did base as I could do that easily. I can change the implementation to pull json from multiple folders fairly easily. However, how do you think of these four groupings? Is each a separate namespace? A separate schema?

[sconsult-ma]

Several questions here:

1. Do we need to support grouping/nesting such as gks-core, etc. So the repository level (in our GitHub prototype) would represent a group of schemas vs. a single schema.
   -- complication in our prototype around permissions which are at the repository level.
2. What is a schema? In GKS, we have yaml files that represent the schema pulled from JSON schema documents.