177 adjacency constraint

[DanielPuthawala]

Closes Issue #177 and Discussion #55.

This pull request serves to formally request review from the Cat-VRS product development group for approval of the
AdjacencyConstraint to draft maturity status and stage it for the next release of Cat-VRS.

Summary of the Pull Request.

Pull Request checklist:

• Does the title of this Pull Request reference the corresponding Issue?
• Is the branch validating against pre-commit hooks? Run pre-commit run --all-files from the root directory.
• Is the branch passing tests? Run pytest tests/ from the root directory.

If the schema or examples were contributed to:

• Were the schema def/ and json/ files recompiled and committed? Run cd schema; make all from the root directory.
• If constraints or recipes were added, have they been added to the readthedocs? To do so, you can revise the appropriate file within docs/source/concepts/.
• Has documentation been regenerated and committed? Run cd docs; make clean watch & from the root directory to compile documentation.
• Have tests been created or updated?

[brendanreardon]

• MultipleKnownGeneElements removed and replaced with gks-core:ConceptSet
• I was able to finally find a BCR::ABL1 fusion with breakpoints online, so that adjacencyEx1 was changed to use this illustrative example in members
• Added Gene Fusion recipe, utilizing a slightly modified description from the VICC Fusion guidelines.
• Regarding Bob Dolin's question about the use of a ConceptSet and categorical variant matching, this may be up to the implementer, I think. Given that the members of the concept set would be connected by an "OR" operator, I can imagine an implementer requiring either (i) if comparing two concept sets, require at least one gene concept to overlap, (ii) if comparing a concept set to a mappable concept, require the gene represented with a mappable concept to be present within the concept set, or (iii) match by default because, by definition, the concept set is non-exhaustive.

Current readthedocs 👇

---

Adjacency Constraint, with MultipleKnownGeneElements replaced with a gks-core:ConceptSet.

Gene Fusion Recipe

[brendanreardon]

Drafted Implementation Guidance for the AdjacencyConstraint. We currently do not have implementation guidance written for any of the Recipes, and this may be more appropriate as Implementation Guidance for the Gene Fusion Recipe.

[brendanreardon]

Additional changes made:

• UnknownGeneElement renamed to UnspecifiedElement
• Added functionalDomains to mimic requirement of VICC Gene Fusion Specification
• Added 4th gene fusion example that includes functional domains

Reached out to Wes for feedback on Functional Domains implementation.

[DanielPuthawala]

Oh good catch!