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monarch-initiative / GENO-ontology

Repository for representing genotypes and their association with phenotypes
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grouping term for population, strain, background, fish, genotype, model? #55

Open sierra-moxon opened 2 years ago

sierra-moxon commented 2 years ago

Data sources use a variety of modeling elements to describe the collection of genetic elements that together produce a particular phenotype or contribute to disease progression.

We'd like one abstract grouping class to collect these various definitions so that we can harmonize the "bag of things" at the organism level, that can be connected to phenotype/disease.

This bag can include: alleles (and variants, though this relationship should be investigated separately), including point mutations, insertions, deletions, deficiencies, rearrangements, etc. transgenes (inserted in the genome via constructs) morpholinos, crisprs, talens, rnai

This bag is sometimes called (depending on various factors as determined by the data source): population strain background fish genotype model

From admittedly naive browsing of GENO in OLS, is the closest mutual parent of these terms is "continuant" in GENO?

We could alternatively handle this in biolink-model via an enumeration of GENO terms.
https://github.com/biolink/biolink-model/issues/1003

matentzn commented 2 years ago

@sierra-moxon I think GENO development is now community - only. No one will likely add classes, unless you do it yourself.. I think you can mention this to @cmungall and if he is fine with it, I can help you add that class.