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biolink / biolink-model

Schema and generated objects for biolink data model and upper ontology
https://biolink.github.io/biolink-model/
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Define the grouping class for population, strain, genotype, background, model, etc. #1003

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 under, 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 variations, though this relationship should be investigated separately) transgenes morpholinos, crisprs, talens, rnai

This bag is sometimes called (depending on various factors that we can enumerate in the model): population strain background genotype model

@RichardBruskiewich @kevinschaper

cmungall commented 2 years ago

Is there a concept in geno?

On Fri, May 6, 2022 at 4:10 PM Sierra Moxon @.***> wrote:

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 under, 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 variations, though this relationship should be investigated separately) transgenes morpholinos, crisprs, talens, rnai

This bag is sometimes called (depending on various factors that we can enumerate in the model): population strain background genotype model

@RichardBruskiewich https://github.com/RichardBruskiewich @kevinschaper https://github.com/kevinschaper

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RichardBruskiewich commented 2 years ago

Is there a concept in geno?

I'll take a closer look at GENO. Here is the synopsis:

sierra-moxon commented 2 years ago

it looks like the closest up the hierachy in GENO that is a parent of all of these is 'continuant.' What if we made a term request in GENO for the grouping term for all of these, made a temporary model component in biolink-model and put in an enumeration in biolink that represents the terms here we want to group.