Problem
The Subject schema currently allows an individual subject to be linked to a species or strain, but it does not provide a field for the subject-specific genotype.
This is problematic in breeding experiments where subjects share the same strain or genetic background but differ in genotype, for example:
These subjects should not need to be represented as separate strains solely because they differ in allele composition or zygosity.
SubjectState is not an ideal location because inherited genotype is generally a stable property of the subject rather than a temporary state.
Proposal
Add an optional genotype property to Subject.
Ideally, this property should support one or more structured genotype entries containing:
- gene or genomic locus
- allele
- zygosity
- human-readable genotype label
Example:
gene: GeneA
allele: mut
zygosity: heterozygous
label: GeneA<mut>/+
Motivation
This would allow openMINDS to distinguish:
- strain or genetic background, represented by
Strain
- subject-specific inherited genotype, represented by
Subject
- temporary physiological or experimental conditions, represented by
SubjectState
It would also support compound genotypes involving multiple modified loci, such as knockout, recombinase-driver, and reporter alleles in the same subject.
🤖 Written with ChatGPT 5.5
Problem
The
Subjectschema currently allows an individual subject to be linked to a species or strain, but it does not provide a field for the subject-specific genotype.This is problematic in breeding experiments where subjects share the same strain or genetic background but differ in genotype, for example:
GeneA<mut>/+GeneA+/+These subjects should not need to be represented as separate strains solely because they differ in allele composition or zygosity.
SubjectStateis not an ideal location because inherited genotype is generally a stable property of the subject rather than a temporary state.Proposal
Add an optional
genotypeproperty toSubject.Ideally, this property should support one or more structured genotype entries containing:
Example:
Motivation
This would allow openMINDS to distinguish:
StrainSubjectSubjectStateIt would also support compound genotypes involving multiple modified loci, such as knockout, recombinase-driver, and reporter alleles in the same subject.
🤖 Written with ChatGPT 5.5