reference and alternate base properties

[nlwashington]

We need some object and/or data properties for listing reference and alternate nucleotide (and/or amino acid) sequences. I could not find any other ontologies that have these.

so to say something like:

my_sequence_alteration has_alternate_nucleotide_sequence 'A'

but the question would be, where would the has_reference_nucleotide go? i don't think we'd want to attach it to the variant.

also, if i want to indicate the downstream impact of the nucleotide change, how would i do that?

my_sequence_alteration results_in_alternate_amino_acid_sequence 'P'

? and/or should the nucleotide/amino acids be classes rather than literals?