Genotype
From WormBaseWiki
Genotype as an object
This page is meant as a chalkboard to throw around ideas and eventually formulate a plan for curating to genotypes and strains rather than individual variations or single genes.
Caltech Group Meeting 19-May-2016 notes
Objectifying Genotypes[edit] Increasingly, we are encountering needs to objectify genotypes We have strain objects, although strains are not always specified in papers We could potentially create strain objects that are named according to a paper ID This would enable us to capture certain phenotype and genetic interaction annotations We need to consider a strain's phenotype in relation to a control strain We already annotate phenotypes to transgenes while specifying the gene (in the transgene) that causes the phenotype It will be good for WB cuartors to hear from other MODs about how they handle this We can reconvene after today's phenotype call and focus on this discussion for future cross-MOD calls
Rationale
Issues
Action items
?Genotype model
Initial proposal:
?Genotype Genotype_name UNIQUE ?Text // e.g. “unc-1(e103);unc-2(e234)”
Genotype_component Gene ?Gene XREF Component_of_genotype #Evidence
Variation ?Variation XREF Component_of_genotype UNIQUE Text // Zygosity
Rearrangement ?Rearrangement XREF Component_of_genotype UNIQUE Text // Zygosity
Transgene ?Transgene XREF Component_of_genotype UNIQUE Text // Zygosity
// Zygosity text entry should be one of the following:
// Homozygous, Heterozygous_with_wildtype, or Heteroallelic_combination
Other_component UNIQUE ?Text // Free text components including RNAi
Disease_info Models_disease ?DO_term XREF Disease_model_genotype
Modifies_disease ?DO_term XREF Disease_modifier_genotype
Disease_model_annotation Model_genotype ?Disease_model_annotation XREF Genotype
Modifier_genotype ?Disease_model_annotation XREF Modifier_genotype
Species UNIQUE ?Species
Remark ?Text
Reference ?Paper XREF Genotype
