We’re working on the Genetic variant archetypes, and have run into an issue with how to represent the more complex positions within a gene. On the genomic level this is easy, a simple positive number starting from the left side of the genome and ending on the right side. For the coding sequence (a single gene), this gets more complicated because positions in the exons are numbered with positive numbers. Positions in the introns are however numbered with a combination of the closest position in the exon, followed by either a plus or minus sign based on whether the right or left exon is closer, and then another number representing the distance from the closest position in the exon (the first number). For example: ‘87+1’ or ‘88-3’.
How should we represent this in archetypes? The simple use case (genomic level) is well represented by a single DV_COUNT, constrained to 1…*. We’d prefer that the same structures be expandable to be usable for the coding sequence examples too.
EDIT: See this background material for more info and examples: https://varnomen.hgvs.org/bg-material/numbering/
Also see this archetype: https://ckm.openehr.org/ckm/archetypes/1013.1.4393. The Start position and End position elements are the ones that are affected by this issue.