Matthew Brush

Nevermind. I think protege is double counting uses of a term. I think we do query them all out afterall.

To support the GA4GH Variant Annotation and ClinVar use case where 'inherited', 'uniparental', and 'biparental' are values used to represent allele origin, I am proposing to add terms reflecting this...

Thanks Chris. I fixed that spurious tab. As for your other points: 1. Good thought about uni/bi parental concepts really being about the allelic complement. The definition in the ontology...

Hi Larry. It is with my GENO hat on that am looking to improve the allele origin hierarchy in the ontology. With my GA4GH-VA hat on, I agree that we...

Considering the discussion and use cases above, I am proposing the following GENO 'allele origin' hierarchy. It includes a few new terms to support ClinVar and ClinGen use cases. ````...

A couple issues were raised for discussion about the proposal above: **1. Do the bi / uniparental terms really apply to the origin of a single allele - as strictly...

Of relevance - the 'Cellular origin of variant' section on p 3 of the ENIGMA article here: https://jmg.bmj.com/content/56/6/347.full

see cgd dataset for use of temp properties created for this ticket

GENO covers lots of concepts related to genotypes, including attributes of variants such as these. We are coordinating with the Sequence Ontology to implement such terms in SO or GENO...

A hierarchy/requirements from our Wormbase contacts (2015-06-02):