From WormBaseWiki
Jump to navigationJump to search

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[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

?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
		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



Action items