WormBase Model:Variation

WormBase Models

Model

//////////////////////////////////////////////////////////////////////////////////////////////
//
//Variation class
//
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?Variation Evidence #Evidence
	   Name Public_name	UNIQUE ?Variation_name XREF Public_name_for
		Other_name	?Variation_name XREF Other_name_for #Evidence
                Rearrangement	?Rearrangement  XREF Variation // some alleles are really rearrangements		
	   Sequence_details SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Allele
			    Flanking_sequences UNIQUE Text UNIQUE Text
			    Mapping_target UNIQUE ?Sequence
			    Source_location UNIQUE Int UNIQUE ?Sequence UNIQUE Int UNIQUE Int UNIQUE #Evidence //source data, <WSversion> ?Sequence pos1 pos2 Evidence(Paper/person etc. remarks)
			    CGH_deleted_probes UNIQUE Text UNIQUE Text
			    CGH_flanking_probes UNIQUE text UNIQUE text
			    Type_of_mutation Substitution UNIQUE Text Text #Evidence // wild type and mutant sequence
					     Insertion    UNIQUE Text      #Evidence
					     Deletion     UNIQUE Text      #Evidence  
					     Inversion
			    PCR_product ?PCR_product XREF Variation  
			    SeqStatus UNIQUE Not_sequenced //[2006-02-17 ar2] to differentiate between mutations which have been sequenced and those which have not.
					     Sequenced
					     Pending_curation
			    Deletion_verification Text #Evidence //[14-Mar-06 ar2] Mark Edgely of KO_alleles has developed test to confirm deletion (mt3)
           Variation_type Allele		
			  SNP            // replaces the old 'Status Text' part of ?Locus model	
			  Confirmed_SNP
			  Predicted_SNP
			  RFLP Reference_strain_digest	 Text Text Text // storing site, enzyme, and band size
			       Polymorphic_strain_digest Text Text Text 
			  Transposon_insertion ?Transposon_family XREF In_variation
			  Natural_variant
	   Origin Species UNIQUE ?Species
		  Strain	 ?Strain XREF Variation #Evidence
		  Laboratory ?Laboratory
		  Author  ?Author // use Person when known, else use Author
                  Person  ?Person //
		  Analysis ?Analysis
		  DB_info Database ?Database ?Database_field UNIQUE ?Text //to link out to KO pages ar2 02-DEC-05
                  KO_consortium_allele   // North American knockout consortium
                  NBP_allele  // Japanese knockout consortium
		  NemaGENETAG_consortium_allele //NemaGENETAG consortium allele - Nektarios et al
		  Detection_method Text
		  Positive_clone ?Clone XREF Positive_variation #Evidence
		  Nature_of_variation UNIQUE Polymorphic
					     Synthetic	
                  History Merged_into UNIQUE ?Variation XREF Acquires_merge //added before WS242?
                          Acquires_merge ?Variation XREF Merged_into
                          Split_from UNIQUE ?Variation XREF Split_into
                          Split_into ?Variation XREF Split_from
		  Status UNIQUE Live #Evidence
                                Suppressed #Evidence
                                Dead #Evidence   
	   Linked_to ?Variation XREF Linked_to  // for being able to specify paired substitutions which are part of the same allele
	   Affects Gene	         ?Gene	     XREF Allele #Molecular_change      //#Molecular_change mh6 define precise changes [060217 ar2]
		   Predicted_CDS ?CDS	     XREF Variation #Molecular_change
		   Transcript    ?Transcript XREF Variation #Molecular_change
		   Pseudogene    ?Pseudogene XREF Variation #Molecular_change
		   Feature       ?Feature    XREF Associated_with_variation
		   Interactor	 ?Interaction
	   Possibly_affects ?Gene XREF Possibly_affected_by #Evidence
           Isolation Date    DateType
                     Mutagen UNIQUE Text #Evidence
                     Forward_genetics Text #Evidence  // Capture the basis of the experiment that isolated
                     Reverse_genetics Text #Evidence  // the allele. [040206 krb]
                     Transposon_excision ?Transposon_family
                     Derived_from ?Variation XREF Derivative
		     Derivative	  ?Variation XREF Derived_from
           Genetics Gene_class ?Gene_class XREF Variation
		    Mating_efficiency  Male UNIQUE ME0_Mating_not_successful #Evidence
						   ME1_Mating_rarely_successful #Evidence
						   ME2_Mating_usually_successful #Evidence
						   ME3_Mating_always_successful #Evidence
				       Hermaphrodite UNIQUE HME0_Mating_not_successful #Evidence
							    HME1_Mating_rarely_successful #Evidence
							    HME2_Mating_usually_successful #Evidence
							    HME3_Mating_always_successful #Evidence
		    Map ?Map   XREF Variation #Map_position
		    Interpolated_map_position UNIQUE ?Map UNIQUE Float
                    Mapping_data 2_point         ?2_point_data
                                 Multi_point     ?Multi_pt_data
                                 Pos_neg_data    ?Pos_neg_data
                                 // above three are for mapping on its own behalf
                                 In_2_point      ?2_point_data
                                 In_multi_point  ?Multi_pt_data
                                 In_pos_neg_data ?Pos_neg_data
                                // these are for when the locus is mapped
		    Marked_rearrangement ?Rearrangement XREF By_variation
	   Description Phenotype ?Phenotype XREF Variation #Phenotype_info
                       Phenotype_remark ?Text #Evidence
		       Phenotype_not_observed ?Phenotype XREF Not_in_Variation #Phenotype_info  //added by Wen to separate Not phenotype from real phenotypes 
                       Nonsense UNIQUE Amber_UAG Text #Evidence
                                       Ochre_UAA Text #Evidence
                                       Opal_UGA  Text #Evidence
                       Missense Text  #Evidence				// text fields stored details of codon change
                       Silent Text #Evidence
                       Splice_site Donor Text #Evidence
                                   Acceptor Text #Evidence
                       Frameshift Text #Evidence  // added sdm
		       Readthrough Text #Evidence // klh WS228
           Reference ?Paper XREF Allele
           Remark  ?Text #Evidence
	   Method UNIQUE ?Method
           Supporting_data Movie   ?Movie   XREF Variation #Evidence  //Carol [060421 ar2] 


?Variation_name Other_name_for     ?Variation XREF Other_name // main reason for this class
                Public_name_for    ?Variation XREF Public_name // the main name for a gene


// hash to contain detailed changes caused by mutations [2006-02-17 ar2]
#Molecular_change   Missense Int    Text #Evidence
                    Silent   Text   #Evidence
                    Nonsense UNIQUE Amber_UAG Text #Evidence
                                    Ochre_UAA Text #Evidence
                                    Opal_UGA  Text #Evidence
				    Ochre_UAA_or_Opal_UGA Text #Evidence
				    Amber_UAG_or_Ochre_UAA Text #Evidence
				    Amber_UAG_or_Opal_UGA Text #Evidence 
                    Splice_site UNIQUE  Donor    Text #Evidence
                                        Acceptor Text #Evidence
                    Frameshift Text #Evidence
                    Readthrough Text #Evidence //klh WS228
                    Intron #Evidence
                    Coding_exon #Evidence
                    Noncoding_exon #Evidence 
		    Promoter #Evidence
		    UTR_3 #Evidence
		    UTR_5 #Evidence 
		    Regulatory_feature #Evidence
		    Genomic_neighbourhood #Evidence

Approved Changes

WS231

Mating_efficiency  Male  UNIQUE ME0_Mating_not_successful
                                ME1_Mating_rarely_successful
                                ME2_Mating_usually_successful
                                ME3_Mating_always_successful
                   Hermaphrodite UNIQUE
                                HE0_Mating_not_successful
                                HE1_Mating_rarely_successful
                                HE2_Mating_usually_successful
                                HE3_Mating_always_successful

Unused tags

Inversion

Nature_of_variation (new)

Polymorphic

Synthetic

Linked_to

Rescued_by_transgene

Phenotype_remark

Haplo_insufficient

Hypermorph

Nonsense

Amber_UAG

Ochre_UAA

Opal_UGA

Missense

Silent

Paternal

Supporting_data

Movie

Picture