-
Notifications
You must be signed in to change notification settings - Fork 10
Variant representation #10
Comments
Apologies, the commit above appears to be unrelated This is what we have as an example:
on the one hand this is scope creep. On the other hand this is practically v useful. The approach is to be modular. The variant part is separable, can be represented outside and referenced, or can be embedded in. Same approach for ped. |
Can someone take a shot at making some fake examples, we will derive the model from this |
@cmungall @pnrobinson @jmcmurry: Why are we not adapting the MME schema for variants? It is fairly comprehensive and would enable PXF to be aligned with it. If you agree, I can have a first stab at implementing it. |
Can you have a go at a PR on the reference implementation? There is also the main GA4GH variant representation. But why don't you On 5 Apr 2016, at 21:18, tudorgroza wrote:
|
Tudor and I just discussed this. I would suggest that we design the format to be easily extensible to other lab abnormalities - say a paper about a protein biomarker and some disease. Or ISCN, glycomics, and metabolomics. Might be a lot for v1 Dr. med. Peter N. Robinson, MSc. Von: Chris Mungall [[email protected]] Can you have a go at a PR on the reference implementation? There is also the main GA4GH variant representation. But why don't you On 5 Apr 2016, at 21:18, tudorgroza wrote:
— |
On 5 Apr 2016, at 22:27, Peter Robinson wrote:
I'm not totally following the relevance to this ticket (other than Just a clarifying note about versions and levels. These are in theory Having said that since we switched to JSON-schema everything is rolled Let's capture some of these requirements e.g. glycomics in separate |
@cmungall : Ok. Can you please have a look at the current PR I've put in? |
Thanks! So Association was originally conceived of as an association between a On 5 Apr 2016, at 23:23, tudorgroza wrote:
|
Thanks. |
I think we shoul leave out the HGVS description - it only applies to humans and we want this to be more generic than that. Also I think we should follow the GA4GH variant schema more closely. The MME one is pretty closely aligned to this anyway. We'll only be able to capture SNPs and indels, but that's the current state of things. We also need the ability to link out to other sources, e.g VCF files. Probably a simple uri will suffice? |
On 6 May 2016, at 3:51, Jules Jacobsen wrote:
That's fine - we will use a genotype object for other scenarios |
We should discuss how to best represent variants. Probably we need something flexible like
HGVS
NM_123:c.-123C>T
with various types that also work for chromosomes, microdeletions, and other sets of findings that might be protein biomarkers etc, so that this standard can be used with a wide range of diseases and publications.
The text was updated successfully, but these errors were encountered: