Clarification on comments re GeneticVariation

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Need clarification on comments re GeneticVariation (row 29)

Current Definition

DEFINITION: The difference(s) in the nucleotide sequence of a biologic entity relative to a reference sequence.

EXAMPLE(S): A single nucleotide change from adenosine to cytosine, of the CAG trinucleotides repeats in the Huntington gene.

OTHER NAME(S):

NOTE(S):

Ballot Comment

genetic reference supports nucleotide and amino acid changes, while the variant only supports nucleotide change. Also examples are not accurate.

Proposed Definition

DEFINITION: The observed sequence relative to the genetic reference sequence.

EXAMPLE(S): TT (nucleotide example) L(amino acid change example)

OTHER NAME(S):

NOTE(S):

Current Disposition

Pending Input From Submitter

Proposed Disposition Comment

Need clarification and coordination with LSDAM SMEs to ensure their intended semantic is accurately represented.

Not clear if this is referencing the GeneticReference class (with which there is no direct association in the model) or if it's a more general use of the term "genetic reference" since this seems to be a comment on the class GeneticVariation. Is this saying GeneticVariation should only be about nucleotide change? If so should there be an amino acid change example? Also the proposed definition change seems to include observed sequences that are NOT variations since it leaves out the term "difference(s)" - is that too broad given the class name?

Outstanding Questions

• Is the proposed definition a fundamental change or expansion of the original concept?
• If so, is this consistent with the LSDAM SMEs intention? (Perhaps GeneticVeriation as defined was just one example of a subclass of a NucleicAcidSequenceFeature.)
• Should we expand the definition or add another subclass instead?
• Should there be a connection between the GeneticVariation class and the GeneticReference class? And if so, what's the nature of the relationship?
• Is this clarifying what's in the model now (in scope for this ballot reconciliation) or adding new semantics (out of scope for this reconciliation effort)?

Responses

Please add your responses here...

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