Stream: genomics
Topic: FYI - GENO value sets!
Larry Babb (Sep 20 2019 at 19:13):
Just sharing that the GENO ontology is now providing well vetted terminology for several of the LOINC codes we previous enumerated answer lists for, which might be better served in the long run by having a reference to an ontological identifier with a much more robust way to express the answers at varying levels of granularity. Matt Brush from Monarch Initiative at OHSU worked on this with others including the ClinGen experts to develop these terms that fall outside of Sequence Ontology yet are pretty essential to this space. They certainly filled some critical gaps for defining genotypes and inheritance patterns.
Here's the mapping of these value sets with those we defined in ClinGen to inform the GENO work (along with a note on a forthcoming Chromosome ontology to provide chromosome identifiers for all organisms - seems like a smart approach for a standard to consider).
Phase Set .
ClinGen allelic phase value set maps to GENO terms here
Allelic State
ClinGen allelic state value set maps to a subset of the GENO terms here
Genomic source (aka Allele Origin)
ClinGen allele origin value set maps to the GENO terms here
Chromsome Ontology (coming very soon!)
Note that we are working on a chromosome ontology that will provider terms for the new Chromosome Value Set I see in your documentation (reference to ClinGen value set). Should be released and accessible via OLS / Ontobee in the next month or two. Github repo is here
Bret H (Sep 24 2019 at 20:55):
Interesting, definite progress : ^ ) but many of these terms exist in other namspaces. Could GENO value sets use terms from LOINC, SNOMED CT, Sequence Ontology? or provide a clear mapping into these standard terminologies?
Last updated: Apr 12 2022 at 19:14 UTC
