Use preferred formats for MappableConcept.mappings

[korikuzma]

Feature description

Use the preferred Coding format for each item in MappableConcept.mappings. A Coding consists of a relation and coding, where a Coding requires:

• code: "A symbol uniquely identifying the concept, as in a syntax defined by the code system. CURIE format is preferred where possible (e.g. 'SO:0000704' is the CURIE form of the Sequence Ontology code for 'gene')."
• system: description": "The terminology/code system that defined the code. May be reported as a free-text name (e.g. 'Sequence Ontology'), but it is preferable to provide a uri/url for the system. When the 'code' is reported as a CURIE, the 'system' should be reported as the uri that the CURIE's prefix expands to (e.g. 'http://purl.obofoundry.org/so.owl/' for the Sequence Ontology)."

Use case

The Coding object allows for flexibility in how system and code are represented, which can lead to inconsistency across different implementations and systems. Aligning these fields to use preferred formats can help ensure consistent representation.

Acceptance Criteria

Given a Mappable Concept (gene) is queried,
When it has mappings,
Then the system must be represented as a URI/URL and the code must be represented as a CURIE, where possible

Proposed solution

No response

Alternatives considered

No response

Implementation details

No response

Potential Impact

No response

Additional context

No response

Contribution

Yes, I can create a PR for this feature.

[jsstevenson]

Might be a nice time to refactor the other (non-normalized) response objects into GKS as well. We'd talked about this a long time ago but never got around to it.

[korikuzma]

@jsstevenson ya, I don't think that's as big of a priority though (at least for VarCat / MetaKB / BMK, since we only use /normalize). Issue is #251

[korikuzma]

So #386 actually really only focused on the system part. Going to create a new PR for using CURIEs for code