Difference between revisions of "Genotype"

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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
      Disease_model_annotation  Model_genotype ?Disease_model_annotation  XREF  Genotype
      Models_disease_in_annotation ?Disease_model_annotation  XREF  Genotype
      Modifier_genotype ?Disease_model_annotation  XREF  Modifier_genotype
          Modifies_disease_in_annotation ?Disease_model_annotation  XREF  Modifier_genotype
Species UNIQUE ?Species
Species UNIQUE ?Species
Remark ?Text                            
Remark ?Text                            

Revision as of 19:33, 24 February 2020


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.


Action items

?Genotype model

Initial proposal:

?Genotype	Genotype_name  UNIQUE  ?Text		//  e.g. “unc-1(e103);unc-2(e234)”; eventually to be automatically generated
                Genotype_synonym   ?Text    // To capture literal representations in the literature
                Genotype_component	Gene	?Gene	  XREF  Component_of_genotype  #Evidence
                                        Variation ?Variation	XREF	Component_of_genotype
		                        Rearrangement	?Rearrangement  XREF	Component_of_genotype
		                        Transgene	?Transgene  XREF  Component_of_genotype
		                        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
			      Models_disease_in_annotation  ?Disease_model_annotation  XREF  Genotype
    			      Modifies_disease_in_annotation  ?Disease_model_annotation  XREF  Modifier_genotype
		Species	UNIQUE ?Species
		Remark	?Text	                           
		Reference	?Paper	XREF	Genotype

Model issues

			      Disease_model_annotation  Model_genotype  ?Disease_model_annotation  XREF  Genotype
    			  				Modifier_genotype  ?Disease_model_annotation  XREF  Modifier_genotype

I don't believe the above fits with the acedb->datomic conversion can we lose the top level Disease_model_annotation tag?

Genotype Postgres Tables

  • gno_identifier
  • gno_curator
  • gno_name
  • gno_synonym
  • gno_gene
  • gno_variation
  • gno_rearrangement
  • gno_transgene
  • gno_othercomp
  • gno_species
  • gno_remark
  • gno_paper
  • gno_nodump

Genotype OA

  • pgid - the postgres ID - NOT DUMPED
  • ID - gno_identifier - Genotype primary ID #Note: This is automatically assigned
  • Curator - gno_curator - NOT DUMPED - Curator (Dropdown)
  • Name - gno_name - Name - Big text
  • Synonym - gno_synonym - Genotype_synonym - Big Text (multiple entries bar "|" separated)
  • Gene - gno_gene - Gene - ?Gene (Multi-ontology)
  • Variation - gno_variation - Variation - ?Variation (Multi-ontology)
  • Rearrangement - gno_rearrangement - Rearrangement - ?Rearrangement (Multi-ontology)
  • Transgene - gno_transgene - Transgene - ?Transgene (Multi-ontology)
  • Other Component - gno_othercomp - Other_component - Big text
  • Species - gno_species - Species - ?Species (Dropdown)
  • Remark - gno_remark - Remark - Big text
  • Paper - gno_paper - Reference - ?Paper (Multi-ontology)
  • NO DUMP - gno_nodump - NOT DUMPED - toggle