Difference between revisions of "Genotype"

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=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.''<br>
 
Caltech Group Meeting [https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls_May_2016#May_19.2C_2016 19-May-2016 notes] <br>
 
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===
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==Rationale==
  
===Issues===
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To enable curators (disease curators and then maybe phenotype curators) to annotate directly to entire genotypes, the ?Genotype class has been proposed. The decision was made that any ?Genotype object should reflect the entire genotype of a particular worm or strain of worms, to the extent that it is known, rather than partial genotypes. The initial data model allows for direct associations to disease model annotations, whereby genotype associations to diseases (DO terms) would then be made during the Postgres curation database dump.
  
===Action items===
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==Issues==
 +
 
 +
==Action items==
  
  
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Reference ?Paper XREF Genotype
 
Reference ?Paper XREF Genotype
 
</pre>
 
</pre>
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== Genotype OA ==

Revision as of 16:00, 19 February 2020

Rationale

To enable curators (disease curators and then maybe phenotype curators) to annotate directly to entire genotypes, the ?Genotype class has been proposed. The decision was made that any ?Genotype object should reflect the entire genotype of a particular worm or strain of worms, to the extent that it is known, rather than partial genotypes. The initial data model allows for direct associations to disease model annotations, whereby genotype associations to diseases (DO terms) would then be made during the Postgres curation database dump.

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


Genotype OA