Difference between revisions of "WormBase Model:Variation"

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(Created page with '__TOC__ WormBase Models == Curator Comments/Description == == Model == <pre> </pre> == Proposed Changes ==')
 
 
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== Model ==
 
== Model ==
 
<pre>
 
<pre>
 +
//////////////////////////////////////////////////////////////////////////////////////////////
 +
//
 +
//Variation class
 +
//
 +
//////////////////////////////////////////////////////////////////////////////////////////////
 +
 +
?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
  
 
</pre>
 
</pre>
  
 
== Proposed Changes ==
 
== Proposed Changes ==
 +
 +
 +
== Approved Changes ==
 +
===WS231===
 +
<pre>
 +
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
 +
</pre>
 +
 +
== 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

Latest revision as of 23:50, 16 April 2014

WormBase Models

Curator Comments/Description

Model

//////////////////////////////////////////////////////////////////////////////////////////////
//
//Variation class
//
//////////////////////////////////////////////////////////////////////////////////////////////

?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

Proposed Changes

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

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