search

clingen-data-model / allele

Documentation for data model of ClinGen
10 stars 2 forks source link

CanonicalAlleleType value list #117

Closed larrybabb closed 9 years ago

larrybabb commented 9 years ago

The canonical allele type should only have two values in the list "nucleotide" and "amino-acid". The current list contains the values that would be a permutation of all of the canonical allele complexity and actual canonical allele types.

Further, the xxx-combined value does not work because a CanonicalAllele could never be both a nucleotide and amino acid, based on the model we have designed.

larrybabb commented 9 years ago

updated CanonicalAlleleType value list to portray the proper two values (copied from the current SimpleAlleleType value list doc).

srynobio commented 9 years ago

I agree about the xxx-combined, for version one, but I think we need to think move it to Milestone 0.2 because we will need to include the type of complex-nucleotide and complex-amino-acid.

larrybabb commented 9 years ago

In order to signify whether a canonical allele is complex or simple, we have a separate "complexity" attribute. The canonical allele type is dedicated to signifying whether or not the canonical allele is amino acid or nucleotide. These are two different cross cutting aspects of the canonical allele class hierarchy. Let's talk more to get to a common understanding.

From: Shawn Rynearson notifications@github.com Reply-To: clingen-data-model/clingen-data-model <reply+000ea21b5fb1793c82967933149b05f277eb0887fa16bebb92cf00000001118f2cd69 2a169ce052adfb0@reply.github.com> Date: Tuesday, June 9, 2015 6:38 PM To: clingen-data-model/clingen-data-model clingen-data-model@noreply.github.com Cc: Lawrence Babb larry.babb@gmail.com Subject: Re: [clingen-data-model] CanonicalAlleleType value list (#117)

Reopened #117 https://github.com/clingen-data-model/clingen-data-model/issues/117 .

‹ Reply to this email directly or view it on GitHub https://github.com/clingen-data-model/clingen-data-model/issues/117#event-3 26841815 .

srynobio commented 9 years ago

I've got it: http://datamodel.clinicalgenome.org/allele/implementation/value_set_list/canonical_allele_complexity.html