WormBase Model:Transgene

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WormBase Models

Curator Comments/Description

== Proposed Updated Model  03 March 2011==

//Proposed Transgene class 03/11 for WS227

?Transgene      Summary UNIQUE ?Text                                 //concise genomic description of the transgene
                Synonym ?Text                                        //for alternative names 
                Promoter  Driven_by_gene ?Gene XREF Drives_transgene //eventually change this tag to promoter_gene 
                          Driven_by_construct  ?Text                 //eventually change this tag to promoter_artificial  
                Reporter  Reporter_product ?Text                     //removed multiple tags for Reporter_product
                          Gene ?Gene XREF Transgene_product Text 
                Reporter_type  ?Text                                 // added for Transcriptional fusion or Translational fusion 
                Construction                                         //new tag to collect the following as subtags
                          Fragment Text ?Text                        //may be deleted later
                          Coinjection_marker ?Text
                          Integration_method UNIQUE ?Text            //changed from Integrated_by                                             
                          Laboratory ?Laboratory #Lab_Location       //changed from Location
                          Author ?Author                             // may eventually be deleted
                Genetic_information                                  //new tag to collect the following as subtags
                         Extrachromosomal                            //new subtag
                         Integrated                                  //new subtag and collects the mapping tags
                             Map ?Map  #Map_position  
                             Map_evidence #Evidence 
                             Mapping_data 2_point ?2_point_data      //if no data, can be removed
                                 Multi_point ?Multi_pt_data          //if no data can be removed
                         Phenotype ?Phenotype XREF Transgene #Phenotype_info
                         Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info  
                Used_for                                             //new tag to collect the following as subtags 
                         Rescue ?Variation XREF Rescued_by_Transgene //removed ?Gene XREF Rescued_by_transgene 
                         Expr_pattern ?Expr_pattern XREF Transgene  
                         Marker_for   ?Text #Evidence 
                         Gene_regulation ?Gene_regulation XREF Transgene 
                         Interactor ?Interaction 
                Associated_with                                      //new tag to collect the following as subtags
                          Marked_rearrangement ?Rearrangement XREF By_transgene
                          Clone ?Clone XREF Transgene Text 
                          Strain ?Strain XREF Transgene 
                Reference ?Paper XREF Transgene  
                Species UNIQUE ?Species       
                Remark ?Text #Evidence                               //contains a lot of construction notes   

== Current Model 03 March 2011 pre-WS227==

//Transgene class from Wen Chen 12/00

?Transgene      Summary UNIQUE ?Text //Searchable description of the transgene
                Synonym ?Text //for alternative names 
                Driven_by Driven_by_gene           ?Gene XREF Drives_transgene
                          Driven_by_construct      ?Text //for artificial promoters     
                Reporter_product GFP //The following tags describe the reporter products
                                 Other_reporter ?Text
                                 Gene ?Gene XREF Transgene_product Text //reporter gene
                Isolation Author ?Author //Authors who created the transgene
                          Clone ?Clone XREF Transgene Text //injected clone conc.
                          Fragment Text Text //injected DNA fragment conc. 
                          Injected_into_CGC_strain ?Strain 
                          Injected_into Text    // for strains not available in CGC
                          Integrated_by UNIQUE Gamma_ray //this is the integration method
                                               Other_integration_method Text 
                Location ?Laboratory #Lab_Location //Which Labs have the transgene.
                Strain ?Strain XREF Transgene //All strains in CGC with the transgene.
                Map ?Map  #Map_position  //map position
                Map_evidence #Evidence //For wen - many papers refer to Transgene, this allows curators to track which is used for mapping
                Mapping_data 2_point ?2_point_data 
                             Multi_point ?Multi_pt_data
                Phenotype ?Phenotype XREF Transgene #Phenotype_info // [2006-04-20 ar2] changed for Carols Phenotype changes
                Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info  //added by Wen separates Not phenotype from phenotype
                Rescue ?Gene XREF Rescued_by_Transgene ?Variation XREF Rescued_by_Transgene //if the transgene rescue a mutant
                Expr_pattern ?Expr_pattern XREF Transgene    //If the transgene is used for Expr_pattern
                Marker_for   ?Text #Evidence //if the transgene is used as a tissue specific marker.
                Marked_rearrangement ?Rearrangement XREF By_transgene
                Gene_regulation ?Gene_regulation XREF Transgene //if the transgenes is used for gene regulation assy
                Interactor ?Interaction //If the transgene is involved in interaction
                Reference ?Paper XREF Transgene     // papers refered to the transgene.
                Species UNIQUE ?Species             // added by krb for consistency with other classes 021030
                Remark ?Text #Evidence              // More comments on the transgene
                Supporting_data Movie ?Movie XREF Transgene #Evidence
                                Picture ?Picture XREF Transgene #Evidence

Proposed Changes

  • Summary -> now only contains concise genomic description of the transgene in brackets\\
  • Rescue -> only XREF ?Variation, not ?Gene\\

Remove tags:

  • Supporting_data ->remove and remove subtags\\
  • Isolation
  • Gamma_ray
  • X_ray
  • Spontaneous
  • UV
  • Particle_bombardment
  • Not_integrated
  • Other_integration_method
  • GFP
  • YFP
  • CFP
  • Venus
  • DsRed
  • mCherry
  • RFP
  • LacZ
  • Other_reporter

New proposed tags:

  • Promoter -> new tag for subtags Driven_by_gene and Driven_by_construct\\
  • Reporter -> new tag to group Reporter_product and Gene **(no change to .ace dumper)**
  • Reporter_type -> new tag for Transcriptional fusion, Translational fusion **(need to add to .ace dumper and OA)**
  • Construction -> new tag to group subtags Fragment, Coinjection_marker, Integration_method
  • Genetic_information -> new tag to group new subtags Extrachromosomal and Integrated
  • Extrachromosomal -> new subtag **(change dumper and OA)**
  • Integrated -> new subtag and groups the mapping tags **(change dumper and OA)** Map, Map_evidence, Mapping_data, 2_point, Multi_point
  • Used_for -> new tag to group Rescue, Expr_pattern, Marker_for, Gene_regulation, Interactor,
  • Associated_with -> new tag to group subtags Marked_rearrangement, Clone, Strain\\

Tag name changes

  • Integration_method -> changed from Integrated_by
  • Laboratory -> changed from Location **(change ace dumper and OA)**

Approved Changes


Reporter 3_UTR ?Gene

Unused tags

2_point -> if nothing in it, remove it\\ Rescue -> changed use of tag, will be used\\ Supporting_data -> remove\\ Movie -> remove\\ Picture -> remove\\