Roadmap

[dosumis]

Roadmap outline

Status: Draft
Order of implementation TBD.

1. Fix basic issues with representation.
   • labelsets as individuals labelsets should be individuals #4
   • existentials to link to cluster (cell set) to CL class Link from cluster to Cell Type should be existential restriction #1
   • Object Properties Property typing issue - pipeline fix needed. #2
2. Reconfigure repo to use LinkML project-generator - this will provide infrastructure for automatically generating multiple representations including JSON schema & Python data classes.
3. Add missing components CAS - use autogeneration from current JSON schema using https://linkml.io/schema-automator/packages/importers.html#importing-from-json-schema -But we will then need some manual editing to bring in other parts of the schema.
4. What other aspects of the schema can we formalise? Favour biolink where possible?
5. Investigate whether we can we support different derived schema versions using LinkML - maybe using LinkML imports?
6. Managing OWL imports - Separate ODK repo to generate ontology modules?

[dosumis]

Hi @hkir-dev,

What it is the status of this repo now? Is the code in the schemauto branch in use or did you migrate all to CAS/CAS-Tools?

I feel that the next step here is to have a repo populated using the generated schema + linkML generators to generate python libs etc. As well as being generally useful, this could be submitted for standards approval (BICAN & scFAIR). We could use this repo for that or start a new one.

re contents of this ticket. - I think these items still need to be tickets.

• Investigate whether we can we support different derived schema versions using LinkML - maybe using LinkML imports?
• Managing OWL imports - Separate ODK repo to generate ontology modules? <-- A v.small ODK repo that generates a helper.owl file would be nice as the RDF files need OWL typing of imported properties to work. I think this is not an issue for loading into KG, but other may wish to inspect/use them independently.

I still like the idea of moving entirely to LinkML as the master schema in future, but this obviously depends on resources.