Difference between revisions of "WormBase Model:Transgene"

From WormBaseWiki
Jump to navigationJump to search
m
Line 22: Line 22:
 
///////////////////////////////////////////////////////////////////////////////  
 
///////////////////////////////////////////////////////////////////////////////  
  
?Transgene      Summary UNIQUE ?Text //Searchable description of the transgene
+
?Transgene      Summary UNIQUE ?Text                                 //concise genomic description of the transgene
                 Synonym ?Text //for alternative names  
+
                 Synonym ?Text                                       //for alternative names  
                 Driven_by  Driven_by_gene     ?Gene XREF Drives_transgene
+
                 Promoter  Driven_by_gene ?Gene XREF Drives_transgene //eventually change this tag to promoter_gene
                           Driven_by_construct  ?Text //for artificial promoters   
+
                           Driven_by_construct  ?Text                 //eventually change this tag to promoter_artificial 
                 Reporter_product   Reporter ?Text  
+
                 Reporter  Reporter_product ?Text                     //removed multiple tags for Reporter_product
                           Gene ?Gene XREF Transgene_product Text //reporter gene
+
                           Gene ?Gene XREF Transgene_product Text  
                 Transgene_type ?Text // Transcriptional fusion or Translational fusion
+
                 Reporter_type ?Text                                 // added for Transcriptional fusion or Translational fusion  
                 Construction (Isolation)
+
                 Construction                                         //new tag to collect the following as subtags
                           Fragment Text ?Text //injected DNA fragment conc. (?)
+
                           Fragment Text ?Text                       //may be deleted later
                           Coinjected_with Coinjection_marker ?Transgene XREF Transgene
+
                           Coinjection_marker ?Text
                           Integrated_by UNIQUE ?Text //the integration method                                              
+
                           Integration_method UNIQUE ?Text           //changed from Integrated_by                                              
                           Location ?Laboratory #Lab_Location //Which lab produced the transgene, assigned automatically based on allele lab designation
+
                           Laboratory ?Laboratory #Lab_Location       //changed from Location
                           Author ?Author //Authors who created the transgene
+
                           Author ?Author                             // may eventually be deleted
                 Genetic_information   Map ?Map  #Map_position  //map position
+
                 Genetic_information                                 //new tag to collect the following as subtags
                        Map_evidence #Evidence //For wen - many papers refer to Transgene. This will allow curators to track which is used for mapping
+
                        Extrachromosomal                            //new subtag
                        Mapping_data 2_point ?2_point_data  
+
                        Integrated                                  //new subtag and collects the mapping tags
                        Multi_point ?Multi_pt_data
+
                            Map ?Map  #Map_position   
                         Phenotype ?Phenotype XREF Transgene #Phenotype_info // [2006-04-20 ar2] changed for Carol's Phenotype changes
+
                            Map_evidence #Evidence  
                         Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info  //added by Wen separates Not phenotype from phenotype
+
                            Mapping_data 2_point ?2_point_data     //if no data, can be removed
                 Used_for Rescue ?Gene XREF Rescued_by_Transgene ?Variation XREF Rescued_by_Transgene //if the transgene rescue a mutant
+
                                Multi_point ?Multi_pt_data         //if no data can be removed
                         Expr_pattern ?Expr_pattern XREF Transgene  //If the transgene is used for Expr_pattern
+
                         Phenotype ?Phenotype XREF Transgene #Phenotype_info
                         Marker_for  ?Text #Evidence //if the transgene is used as a tissue specific marker.
+
                         Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info   
                         Gene_regulation ?Gene_regulation XREF Transgene //if the transgene is used for gene regulation assay
+
                 Used_for Rescue                                     //new tag to collect the following as subtags
                         Interactor ?Interaction //If the transgene is involved in interaction
+
                        ?Variation XREF Rescued_by_Transgene       //removed ?Gene XREF Rescued_by_transgene
                        Coinjection_marker Coinjected_with ?Transgene  XREF Transgene //not dumped, people do not use proper name
+
                         Expr_pattern ?Expr_pattern XREF Transgene   
                Associated_with  Marked_rearrangement ?Rearrangement XREF By_transgene
+
                         Marker_for  ?Text #Evidence  
                           Clone ?Clone XREF Transgene Text //injected clone conc.(?)
+
                         Gene_regulation ?Gene_regulation XREF Transgene  
                           Strain ?Strain XREF Transgene //All strains with the transgene. **REMOVE?? transgenes XREF in Strain, only CGC strains will show**
+
                         Interactor ?Interaction  
                 Reference ?Paper XREF Transgene   // papers referring to transgene.
+
                Associated_with                                      //new tag to collect the following as subtags
                 Species UNIQUE ?Species           // added by krb for consistency with other classes 021030
+
                          Marked_rearrangement ?Rearrangement XREF By_transgene
                 Remark ?Text #Evidence           // More comments on the 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 
  
 
</pre>
 
</pre>

Revision as of 22:25, 31 March 2011

WormBase Models

Curator Comments/Description

== Proposed Updated Model  03 March 2011 ==

///////////////////////////////////////////////////////////////////////////////
//Proposed Transgene class 03/11
/////////////////////////////////////////////////////////////////////////////// 

?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 Rescue                                      //new tag to collect the following as subtags 
                         ?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==

///////////////////////////////////////////////////////////////////////////////
//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
                                 YFP 
                                 CFP 
                                 Venus
                                 DsRed
                                 mCherry
                                 RFP
                                 LacZ
                                 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
                                               X_ray
                                               Spontaneous
                                               UV
                                               Particle_bombardment
                                               Not_integrated
                                               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

Unused tags

2_point

Rescue

Supporting_data

Movie

Picture