Difference between revisions of "Genotype"

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=Genotype as an object=
 
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''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.''<br>
 
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Caltech Group Meeting [http://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#May_19.2C_2016 19-May-2016 notes] <br>
 
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Objectifying Genotypes[edit]
 
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Increasingly, we are encountering needs to objectify genotypes
 
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We have strain objects, although strains are not always specified in papers
 
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We could potentially create strain objects that are named according to a paper ID
 
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This would enable us to capture certain phenotype and genetic interaction annotations
 
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We need to consider a strain's phenotype in relation to a control strain
 
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We already annotate phenotypes to transgenes while specifying the gene (in the transgene) that causes the phenotype
 
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It will be good for WB cuartors to hear from other MODs about how they handle this
 
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We can reconvene after today's phenotype call and focus on this discussion for future cross-MOD calls
 
  
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===Rationale===
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==Rationale==
  
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===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 (curated in the disease OA), whereby genotype associations to diseases (DO terms) would then be made during the Postgres curation database dump.
  
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===Action items===
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==Issues==
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==Action items==
  
  
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                        // Homozygous, Heterozygous_with_wildtype, or Heteroallelic_combination
 
                        // Homozygous, Heterozygous_with_wildtype, or Heteroallelic_combination
 
                        Other_component UNIQUE  ?Text  // Free text components including RNAi
 
                        Other_component UNIQUE  ?Text  // Free text components including RNAi
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Is_genotype_for_strain ?Strain XREF Genotype
 
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Has_background_strain  UNIQUE  ?Strain  XREF  Is_background_for // Only use when NOT N2
 
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Relation_to_other_genotypes   Has_maternal_genotype UNIQUE ?Genotype XREF Is_maternal_genotype_for
 
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  Has_paternal_genotype UNIQUE ?Genotype XREF Is_paternal_genotype_for
 
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    Is_maternal_genotype_for ?Genotype XREF Has_maternal_genotype
 
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  Is_paternal_genotype_for ?Genotype XREF Has_paternal_genotype
 
 
Disease_info  Models_disease  ?DO_term  XREF  Disease_model_genotype
 
Disease_info  Models_disease  ?DO_term  XREF  Disease_model_genotype
 
      Modifies_disease  ?DO_term  XREF  Disease_modifier_genotype
 
      Modifies_disease  ?DO_term  XREF  Disease_modifier_genotype
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Reference ?Paper XREF Genotype
 
Reference ?Paper XREF Genotype
 
</pre>
 
</pre>
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== Genotype Postgres Tables ==
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*gen_identifier
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*gen_curator
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*gen_name
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*gen_gene
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*gen_variation
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*gen_homo_variation
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*gen_hetwt_variation
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*gen_hetal_variation
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*gen_rearrangement
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*gen_homo_rearrangement
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*gen_hetwt_rearrangement
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*gen_hetal_rearrangement
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*gen_transgene
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*gen_homo_transgene
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*gen_hetwt_transgene
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*gen_hetal_transgene
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*gen_othercomp
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*gen_species
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*gen_remark
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*gen_paper
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*gen_nodump
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== Genotype OA ==
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*pgid - the postgres ID - NOT DUMPED
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*ID - gen_identifier - Genotype primary ID #Note: This is automatically assigned
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*Curator - gen_curator - NOT DUMPED - Curator (Dropdown)
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*Name - gen_name - Name - Big text
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*Gene - gen_gene - Gene - ?Gene (Ontology)
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*Variation (Unknown Zygosity) - gen_variation - Variation - ?Variation  (Multi-ontology)
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*Homozygous Variation - gen_homo_variation - Variation - ?Variation  Homozygous  (Multi-ontology)
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*Heterozygous (w/WT) Variation - gen_hetwt_variation - Variation - ?Variation  Heterozygous_with_wildtype  (Multi-ontology)
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*Heteroallelic Variation - gen_hetal_variation - Variation - ?Variation  Heteroallelic_combination  (Multi-ontology)
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*Rearrangement (Unknown Zygosity) - gen_rearrangement - Rearrangement - ?Rearrangement  (Multi-ontology)
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*Homozygous Rearrangement - gen_homo_rearrangement - Rearrangement - ?Rearrangement  Homozygous  (Multi-ontology)
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*Heterozygous (w/WT) Rearrangement - gen_hetwt_rearrangement - Rearrangement - ?Rearrangement  Heterozygous_with_wildtype  (Multi-ontology)
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*Heteroallelic Rearrangement - gen_hetal_rearrangement - Rearrangement - ?Rearrangement  Heteroallelic_combination  (Multi-ontology)
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*Transgene (Unknown Zygosity) - gen_transgene - Transgene - ?Transgene  (Multi-ontology)
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*Homozygous Transgene - gen_homo_transgene - Transgene - ?Transgene  Homozygous  (Multi-ontology)
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*Heterozygous (w/WT) Transgene - gen_hetwt_transgene - Transgene - ?Transgene  Heterozygous_with_wildtype  (Multi-ontology)
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*Heteroallelic Transgene - gen_hetal_transgene - Transgene - ?Transgene  Heteroallelic_combination  (Multi-ontology)
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*Other Component - gen_othercomp - Other_component - Big text
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*Species - gen_species - Species - ?Species (Dropdown)
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*Remark - gen_remark - Remark - Big text
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*Paper - gen_paper - Reference - ?Paper (Ontology)
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*NO DUMP - gen_nodump - NOT DUMPED - toggle

Revision as of 19:57, 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 (curated in the disease OA), 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 Postgres Tables

  • gen_identifier
  • gen_curator
  • gen_name
  • gen_gene
  • gen_variation
  • gen_homo_variation
  • gen_hetwt_variation
  • gen_hetal_variation
  • gen_rearrangement
  • gen_homo_rearrangement
  • gen_hetwt_rearrangement
  • gen_hetal_rearrangement
  • gen_transgene
  • gen_homo_transgene
  • gen_hetwt_transgene
  • gen_hetal_transgene
  • gen_othercomp
  • gen_species
  • gen_remark
  • gen_paper
  • gen_nodump


Genotype OA

  • pgid - the postgres ID - NOT DUMPED
  • ID - gen_identifier - Genotype primary ID #Note: This is automatically assigned
  • Curator - gen_curator - NOT DUMPED - Curator (Dropdown)
  • Name - gen_name - Name - Big text
  • Gene - gen_gene - Gene - ?Gene (Ontology)
  • Variation (Unknown Zygosity) - gen_variation - Variation - ?Variation (Multi-ontology)
  • Homozygous Variation - gen_homo_variation - Variation - ?Variation Homozygous (Multi-ontology)
  • Heterozygous (w/WT) Variation - gen_hetwt_variation - Variation - ?Variation Heterozygous_with_wildtype (Multi-ontology)
  • Heteroallelic Variation - gen_hetal_variation - Variation - ?Variation Heteroallelic_combination (Multi-ontology)
  • Rearrangement (Unknown Zygosity) - gen_rearrangement - Rearrangement - ?Rearrangement (Multi-ontology)
  • Homozygous Rearrangement - gen_homo_rearrangement - Rearrangement - ?Rearrangement Homozygous (Multi-ontology)
  • Heterozygous (w/WT) Rearrangement - gen_hetwt_rearrangement - Rearrangement - ?Rearrangement Heterozygous_with_wildtype (Multi-ontology)
  • Heteroallelic Rearrangement - gen_hetal_rearrangement - Rearrangement - ?Rearrangement Heteroallelic_combination (Multi-ontology)
  • Transgene (Unknown Zygosity) - gen_transgene - Transgene - ?Transgene (Multi-ontology)
  • Homozygous Transgene - gen_homo_transgene - Transgene - ?Transgene Homozygous (Multi-ontology)
  • Heterozygous (w/WT) Transgene - gen_hetwt_transgene - Transgene - ?Transgene Heterozygous_with_wildtype (Multi-ontology)
  • Heteroallelic Transgene - gen_hetal_transgene - Transgene - ?Transgene Heteroallelic_combination (Multi-ontology)
  • Other Component - gen_othercomp - Other_component - Big text
  • Species - gen_species - Species - ?Species (Dropdown)
  • Remark - gen_remark - Remark - Big text
  • Paper - gen_paper - Reference - ?Paper (Ontology)
  • NO DUMP - gen_nodump - NOT DUMPED - toggle
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