Difference between revisions of "WormBase Model:Transgene"

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                 Driven_by Driven_by_gene          ?Gene XREF Drives_transgene
 
                 Driven_by Driven_by_gene          ?Gene XREF Drives_transgene
 
                           Driven_by_construct      ?Text //for artificial promoters     
 
                           Driven_by_construct      ?Text //for artificial promoters     
                 Reporter_product GFP //The following tags describe the reporter products
+
                 Reporter_product '''GFP''' //The following tags describe the reporter products
                                 YFP  
+
                                 '''YFP  
 
                                 CFP  
 
                                 CFP  
 
                                 Venus
 
                                 Venus
Line 66: Line 66:
 
                                 mCherry
 
                                 mCherry
 
                                 RFP
 
                                 RFP
                                 LacZ
+
                                 LacZ'''
 
                                 Other_reporter ?Text
 
                                 Other_reporter ?Text
 
                                 Gene ?Gene XREF Transgene_product Text //reporter gene
 
                                 Gene ?Gene XREF Transgene_product Text //reporter gene
Line 74: Line 74:
 
                           Injected_into_CGC_strain ?Strain  
 
                           Injected_into_CGC_strain ?Strain  
 
                           Injected_into Text    // for strains not available in CGC
 
                           Injected_into Text    // for strains not available in CGC
                           Integrated_by UNIQUE Gamma_ray //this is the integration method
+
                           Integrated_by UNIQUE '''Gamma_ray''' //this is the integration method
                                               X_ray
+
                                               '''X_ray
 
                                               Spontaneous
 
                                               Spontaneous
 
                                               UV
 
                                               UV
 
                                               Particle_bombardment
 
                                               Particle_bombardment
 
                                               Not_integrated
 
                                               Not_integrated
                                               Other_integration_method Text  
+
                                               Other_integration_method Text'''
 
                 Location ?Laboratory #Lab_Location //Which Labs have the transgene.
 
                 Location ?Laboratory #Lab_Location //Which Labs have the transgene.
 
                 Strain ?Strain XREF Transgene //All strains in CGC with the transgene.
 
                 Strain ?Strain XREF Transgene //All strains in CGC with the transgene.
 
                 Map ?Map  #Map_position  //map position
 
                 Map ?Map  #Map_position  //map position
                 Map_evidence #Evidence //For wen - many papers refer to Transgene. This will allow curators to track which is used for mapping
+
                 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  
 
                 Mapping_data 2_point ?2_point_data  
 
                             Multi_point ?Multi_pt_data
 
                             Multi_point ?Multi_pt_data
 
                 Phenotype ?Phenotype XREF Transgene #Phenotype_info // [2006-04-20 ar2] changed for Carols Phenotype changes
 
                 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 to separate Not phenotype from real phenotypes
+
                 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
 
                 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
+
                 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.
 
                 Marker_for  ?Text #Evidence //if the transgene is used as a tissue specific marker.
 
                 Marked_rearrangement ?Rearrangement XREF By_transgene
 
                 Marked_rearrangement ?Rearrangement XREF By_transgene
 
                 Gene_regulation ?Gene_regulation XREF Transgene //if the transgenes is used for gene regulation assy
 
                 Gene_regulation ?Gene_regulation XREF Transgene //if the transgenes is used for gene regulation assy
 
                 Interactor ?Interaction //If the transgene is involved in interaction
 
                 Interactor ?Interaction //If the transgene is involved in interaction
                 Reference ?Paper XREF Transgene                                                 // papers refered to the transgene.
+
                 Reference ?Paper XREF Transgene     // papers refered to the transgene.
                 Species UNIQUE ?Species                                                         // added by krb for consistency with other classes 021030
+
                 Species UNIQUE ?Species             // added by krb for consistency with other classes 021030
                 Remark ?Text #Evidence                                                           // More comments on the transgene
+
                 Remark ?Text #Evidence             // More comments on the transgene
                 Supporting_data Movie ?Movie XREF Transgene #Evidence
+
                 '''Supporting_data Movie ?Movie XREF Transgene #Evidence
                                 Picture ?Picture XREF Transgene #Evidence
+
                                 Picture ?Picture XREF Transgene #Evidence'''
  
 
</pre>
 
</pre>

Revision as of 17:39, 31 March 2011

WormBase Models

Curator Comments/Description

Proposed Updated Model 03 March 2011

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

?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    Reporter ?Text 
                          Gene ?Gene XREF Transgene_product Text //reporter gene
                Transgene_type  ?Text // Transcriptional fusion or Translational fusion
                Construction (Isolation)
                          Fragment Text ?Text //injected DNA fragment conc. (?)
                          Coinjected_with Coinjection_marker ?Transgene XREF Transgene
                          Integrated_by UNIQUE ?Text //the integration method                                             
                          Location ?Laboratory #Lab_Location //Which lab produced the transgene, assigned automatically based on allele lab designation
                          Author ?Author //Authors who created the transgene
                Genetic_information   Map ?Map  #Map_position  //map position
                         Map_evidence #Evidence //For wen - many papers refer to Transgene. This will allow 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 Carol's Phenotype changes
                         Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info  //added by Wen separates Not phenotype from phenotype
                Used_for 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.
                         Gene_regulation ?Gene_regulation XREF Transgene //if the transgene is used for gene regulation assay
                         Interactor ?Interaction //If the transgene is involved in interaction
                         Coinjection_marker Coinjected_with ?Transgene  XREF Transgene //not dumped, people do not use proper name 
                Associated_with   Marked_rearrangement ?Rearrangement XREF By_transgene
                          Clone ?Clone XREF Transgene Text //injected clone conc.(?)
                          Strain ?Strain XREF Transgene //All strains with the transgene. **REMOVE?? transgenes XREF in Strain, only CGC strains will show**
                Reference ?Paper XREF Transgene   // papers referring to transgene.
                Species UNIQUE ?Species           // added by krb for consistency with other classes 021030
                Remark ?Text #Evidence            // More comments on the transgene

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