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Genotype as an object
This page is meant as a chalkboard to through 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 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
?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 Is_genotype_for_strain ?Strain XREF Genotype Has_background_strain UNIQUE ?Strain XREF Is_background_for // Only use when NOT N2 Relation_to_other_genotypes Has_maternal_genotype UNIQUE ?Genotype XREF Is_maternal_genotype_for Has_paternal_genotype UNIQUE ?Genotype XREF Is_paternal_genotype_for Is_maternal_genotype_for ?Genotype XREF Has_maternal_genotype Is_paternal_genotype_for ?Genotype XREF Has_paternal_genotype 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