Value Set definitions for v0 release

[mbrush]

It will be important to standardize data for certain attributes by binding them to value sets. We identified a handful of places where we considered this (see below), and agreed on terms to be included in a handful of high priority value sets - but we have yet to document these formally. We need to decide if/where/how we will provide recommended value sets in the v0 VA-Spec release, and document these value sets in a more formal way.

Proposal: Document high value/priority value sets informally for v0, but do not require use of these in v0 release

Next Steps: Create central documentation of value sets in scope for v0, and decide on representational format (in spreadsheet? text/yaml file? describe using FHIR or SEPIO value set models?)

Value Sets relevant for v0 statements:

• Molecular Consequence - descriptor of Molecular Consequence Statement. Use SO, but need to decide if we will leave it at this, or define a recommended subset of terms.
• Topological Relationship - predicate of Relative Location Statement use defined subset of RO under 'sequentially related to' (link)
• Variant Origin - qualifier on Pathogenicity, Therapeutic Intervention, RCV and VCV Aggregate Significance Statements . . . use terms under 'allele origin' in the Genotype Ontology (link)?
• Variant Pathogenicity - predicate of Pathogenicity Statements . . . use terms from LOINC or GENO representing 5 ACMG levels (e.g. 'pathogenic')?
• Pathogenic Mechanism - qualifier on Pathogenicity Statements . . . I think we decided no value set here - possible values too varied. And t.b.h. I cannot recall what the use case was for this qualifier?
• Therapeutic Response - for Therapeutic Intervention Statements . . . use a defined set of terms in house (see proposals in #33)
• Disease - a component of a Genetic Condition . . . consider recommending one or more ontologies/terminologies (e.g. MONDO)
• Phenotype - a component of a Genetic Condition . . . consider recommending one or more ontologies/terminologies (e.g. HPO)
• Mode of Inheritance - an attribute of a Genetic Condition . . . consider recommending inheritance pattern terms in HPO and/or GENO
• Gene - a component of a Genetic Condition . . . provide a list of recommended identifier systems? with priority ranking?

[mbrush]

Proposal: For v0 release - informally describe value sets in our modeling spreadsheet.

For v1, define a formal representation as part of the spec. Some examples to inform this work may include the FHIR Value Set resource definition, and the SEPIO value set model.