Difference between revisions of "WormBase Model:Transgene"

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== Model ==
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== Proposed Updated Model 03 March 2011 ==
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<pre>
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///////////////////////////////////////////////////////////////////////////////
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//Transgene class from Wen Chen 12/00
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///////////////////////////////////////////////////////////////////////////////
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?Transgene      Summary UNIQUE ?Text //Searchable description of the transgene
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                Synonym ?Text //for alternative names
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                Driven_by Driven_by_gene          ?Gene XREF Drives_transgene
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                          Driven_by_construct      ?Text //for artificial promoters   
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                Reporter_product Reporter ?Text
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                                Gene ?Gene XREF Transgene_product Text //reporter gene
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                Isolation Author ?Author //Authors who created the transgene
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                          Clone ?Clone XREF Transgene Text //injected clone conc.
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                          Fragment Text Text //injected DNA fragment conc.
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                          Injected_into_CGC_strain ?Strain
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                          Injected_into Text    // for strains not available in CGC
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                          Integrated_by UNIQUE ?Text //the integration method                                           
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                Location ?Laboratory #Lab_Location //Which Labs have the transgene.
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                Strain ?Strain XREF Transgene //All strains in CGC with the transgene.
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                Map ?Map  #Map_position  //map position
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                Map_evidence #Evidence //For wen - many papers refer to Transgene. This will allow curators to track which is used for mapping
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                Mapping_data 2_point ?2_point_data
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                            Multi_point ?Multi_pt_data
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                Phenotype ?Phenotype XREF Transgene #Phenotype_info // [2006-04-20 ar2] changed for Carols Phenotype changes
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                Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info  //added by Wen to separate Not phenotype from real phenotypes
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                Rescue ?Gene XREF Rescued_by_Transgene ?Variation XREF Rescued_by_Transgene //if the transgene rescue a mutant
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                Expr_pattern ?Expr_pattern XREF Transgene                                        //If the transgene is used for Expr_pattern
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                Marker_for  ?Text #Evidence //if the transgene is used as a tissue specific marker.
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                Marked_rearrangement ?Rearrangement XREF By_transgene
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                Gene_regulation ?Gene_regulation XREF Transgene //if the transgenes is used for gene regulation assy
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                Interactor ?Interaction //If the transgene is involved in interaction
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                Reference ?Paper XREF Transgene                                                  // papers refered to the transgene.
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                Species UNIQUE ?Species                                                          // added by krb for consistency with other classes 021030
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                Remark ?Text #Evidence                                                          // More comments on the transgene
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</pre>
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 +
 
 +
== Current Model 03 March 2011==
 
<pre>
 
<pre>
 
///////////////////////////////////////////////////////////////////////////////
 
///////////////////////////////////////////////////////////////////////////////

Revision as of 02:32, 3 March 2011

WormBase Models

Curator Comments/Description

Proposed Updated 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 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 ?Text //the integration method                                             
                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 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 Carols Phenotype changes
                Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info  //added by Wen to separate Not phenotype from real phenotypes
                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


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 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 Carols Phenotype changes
                Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info  //added by Wen to separate Not phenotype from real phenotypes
                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

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