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
 +
                            CGH_deleted_probes UNIQUE Text UNIQUE Text
 +
                            FivePrimeGap      UNIQUE Int
 +
                            ThreePrimeGap      UNIQUE Int                           
 +
                            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
 +
                  Laboratory ?Laboratory XREF Alleles
 +
                  Author  ?Author // use Person when known, else use Author
 +
                  Person  ?Person //
 +
                  DB_info    Database ?Database ?Database_field UNIQUE ?Accession_number //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 
 +
                  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
 +
                    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
 +
                    Rescued_by_transgene ?Transgene     
 +
                    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
 +
          Reference ?Paper XREF Allele
 +
          Remark  ?Text #Evidence
 +
          Method UNIQUE ?Method
 +
          Supporting_data Movie  ?Movie  XREF Variation #Evidence  //Carol [060421 ar2]
 +
                          Picture ?Picture XREF Variation #Evidence
 +
 +
 +
?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
 +
                    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 ==

Revision as of 09:26, 10 August 2010

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
                            CGH_deleted_probes UNIQUE Text UNIQUE Text
                            FivePrimeGap       UNIQUE Int
                            ThreePrimeGap      UNIQUE Int                             
                            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
                  Laboratory ?Laboratory XREF Alleles
                  Author  ?Author // use Person when known, else use Author
                  Person  ?Person //
                  DB_info    Database ?Database ?Database_field UNIQUE ?Accession_number //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  
                  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
                    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
                    Rescued_by_transgene ?Transgene      
                    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
           Reference ?Paper XREF Allele
           Remark  ?Text #Evidence
           Method UNIQUE ?Method
           Supporting_data Movie   ?Movie   XREF Variation #Evidence  //Carol [060421 ar2] 
                           Picture ?Picture XREF Variation #Evidence


?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
                    Intron #Evidence
                    Coding_exon #Evidence
                    Noncoding_exon #Evidence 
                    Promoter #Evidence
                    UTR_3 #Evidence
                    UTR_5 #Evidence 
                    Regulatory_feature #Evidence
                    Genomic_neighbourhood #Evidence

Proposed Changes

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