Hi everyone! 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…

[image] siljelb: So it seems like our solution is to use DV_PARSABLE. After today’s meeting, we’ve decided to reverse this decision. The original intent of the specific variant clusters was to be able to work with the atomic data on the genomic sequence level without having to unpack the HGVS…

If combinations are finite (are they?), maybe a mini terminology can be defined with all combinations. Probably would ease translation to make it readable

Hi Diego! Combinations aren’t finite, as far as I understand. Also, we’d like to be able to use the data to identify the actual numeric position in the gene or genome, and I think a terminology would be less useful for that.

At least for the genetic variation, why not just handle it as parsable text. I see parallels with the ISO Duration types - sometimes a wee parsable string is the easiest way to go. I’m not sure I see the value in splitting it up in an archetype. This is a way of encoding the position but ? in a pre…

Hi all, regarding the genetic use case, the way in which the position of a mutation is expressed depends on the reference sequence we are using to describe the variation. The easy case is when we’re using a genomic (g.) sequence and a positive integer is enough to locate the mutation in the genome…

it can be part of the constraint on the type. We can be as strict as we want: just generalizing for this last case e.g. [a-z]\.[\+\-\*]?[1-9][0-9]+([\+\-\*][1-9][0-9]+)? where [a-z]\. is = g.|c.|etc. (can be nailed to exact letters?) [\+\-\*]? modifier [1-9][0-9]+ an integer probably needs more…

What Cecilia says! She is coordinating the SMEs from the content point of view and is the source of truth for the model content. I am absolutely no genomics expert :blush: Silje & I are merely trying to understand enough of the content in order to suggest the best way to represent the data… @ce.m…

[image] ian.mcnicoll: At least for the genetic variation, why not just handle it as parsable text. I see parallels with the ISO Duration types - sometimes a wee parsable string is the easiest way to go. I’m not sure I see the value in splitting it up in an archetype. This is a way of encoding th…

Legal in ADL, not sure of tooling support if that’s the question

YesDV_PARSABLE allows you tp specify the ‘formalism’ as well as the string of text. So something like { formalism :“HGVS-Varint -nomenclature” value: " c.*37-3" } It might be possible to do some validation using regex but arguably whether there is added value. @Silje - I’d keep everything in…

Representation of genetic positions

Clinical

damoca (David Moner) 4 March 2020 11:02 4

Several years ago, in the conclusions of my Master Thesis, I reasoned about the need of developing specific data types for genetic information. This combined with some low-level archetypes (CLUSTERs) would be an interesting research topic.

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Representation of genetic positions

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