Matthew Brush

I reviewed several tickets (#2, #6, #18) relating to the issue of defining a hierarchy of phenotypic inheritance classes in GENO, to describe the mode of inheritance of traits/phenotypes/diseases. As...

Also of note, some of the terms requested for OMIA seem to conflate inheritance and other aspects of phenotype manifestation. For example 'Autosomal dominant with variable expressivity'. Should this be...

Translating Melissa's feedback from our discussion today: - prefers Proposal 1 of classifying along multiple dimensions and creating defined classes to get a polyhierarchy with inferred multiple inheritance to the...

Hi @rctauber. A few new inheritance-related classes have made their way into GENO, but nothing approaching the full proposal specced out above. We could probably push forward on this if...

Hi @rctauber. Sorry for dropping the ball here - I haven't had a chance to sync up with @mellybelly and @pnrobinson on this yet. But I think there is general...

I removed the molecular function import from GENO, as it was there for exploratory purposes and is not needed. To deal with the 'has role' issue, for now I created...

The notion of a genotype as defined in GENO describes variation in the state of the genome of a particular cell. When a genotype is linked to an organism, there...

Started looking through these various pieces of documentation and code. Some thoughts here to clarify the scope and goals for the phenopackets context file. I see three types of mappings...

@cmungall what is timeline for needing this? I'm assuming it is not needed for the publication?

Some of the issues in the the google doc below are relevant here The doc compares different approaches for representing G2P associations involving molecular phenotypes: https://docs.google.com/document/d/1Aaas-Eip5JCgPQ7taFR62Cj3GlF8oL4n6dQhvxTX3qg/edit#