WormBase Model:Transgene

From WormBaseWiki
Jump to: navigation, search

WormBase Models

Curator Comments/Description

Updated model for WS245

?Transgene      Evidence #Evidence
		Public_name UNIQUE ?Text
		Summary UNIQUE ?Text
		Synonym ?Text
		Corresponding_variation UNIQUE ?Variation XREF Corresponding_transgene //put in to unambiguously associate the allele/transgene
		Construction Construct   ?Construct XREF Transgene_construct
     			     Coinjection ?Construct XREF Transgene_coinjection
     			     Coinjection_other ?Text //for coinjection markers that are not specified as a construct
     			     Integration_method UNIQUE ?Text
     			     Integrated_from ?Transgene XREF Transgene_derivation
     			     Laboratory ?Laboratory #Lab_Location
     			     Author ?Author
		Construction_summary ?Text
		Genetic_information Extrachromosomal
				    Integrated
				    Map ?Map  #Map_position  //needed for transgenes with no granular mapping, e.g., just mapped to a LG
                                              Mapping_data 2_point ?2_point_data      //deleted for WS245, rolled back for WS246
				    Map_evidence #Evidence
				    Phenotype ?Phenotype XREF Transgene #Phenotype_info
				    Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info
		Used_for Transgene_derivation ?Transgene XREF Integrated_from
			 Expr_pattern ?Expr_pattern XREF Transgene
			 Marker_for   ?Text #Evidence
			 Interactor ?Interaction
		Associated_with Marked_rearrangement ?Rearrangement XREF By_transgene
				Strain ?Strain XREF Transgene
		Reference ?Paper XREF Transgene
		Species UNIQUE ?Species
		Remark ?Text #Evidence
                Historical_gene   ?Gene #Evidence

Pre WS245 model

 ?Transgene	Evidence	#Evidence
        Public_name //added for WS234
 	Summary	UNIQUE	?Text
 	Synonym	?Text
 	Promoter	Driven_by_gene	?Gene	XREF	Drives_Transgene
 		Driven_by_construct	?Text
 	Reporter	Reporter_product	?Text
 		Gene	?Gene	XREF	Transgene_product	Text
                3_UTR  ?Gene   
 	Reporter_type	?Text
 	Construction	Fragment	?Text
 		Coinjection_marker	?Text
 		Integration_method	UNIQUE	?Text
 		Laboratory	?Laboratory	#Lab_Location
 		Author	?Author
 		Person	?Person
 	Genetic_information	Extrachromosomal
 		Integrated
 		Map	?Map	#Map_position
 		Map_evidence	#Evidence
 		Mapping_data	2_point	?2_point_data
 			Multi_point	?Multi_pt_data
 		Phenotype	?Phenotype	XREF	Transgene	#Phenotype_info
 		Phenotype_not_observed	?Phenotype	XREF	Not_in_Transgene	#Phenotype_info
 	Used_for	
 		Expr_pattern	?Expr_pattern	XREF	Transgene
 		Marker_for	?Text	#Evidence
 		Gene_regulation	?Gene_regulation	XREF	Transgene
 		Interactor	?Interaction
 	Associated_with	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

--kjy 00:16, 26 May 2012 (UTC)

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 
                          3_UTR ?Gene
                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   


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
                                 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

Approved Changes

WS251

Transgene_for_disease	?DO_term	XREF	Associated_transgene	#Evidence

WS238

Historical gene tags added by Chris
 Promoter  Driven_by_gene ?Gene XREF Drives_transgene		// eventually change this tag to promoter_gene
 Promoter  Driven_by_gene ?Gene XREF Drives_transgene #Evidence // eventually change this tag to promoter_gene
 Gene ?Gene XREF Transgene_product Text
 Gene ?Gene XREF Transgene_product #Evidence 
 3_UTR  ?Gene
 3_UTR  ?Gene #Evidence

WS237

Construction_summary Text //To keep in sync with website tags - moved all Remark info to Construction Summary. Remark comments are by default hidden in the overview widget

WS234

 Public_name //Added to implement WBTransgeneID as main object name. Necessary for resolving duplications/ambiguities resulting from cross curation with expression pattern and gene regulation.

WS233

Reporter 3_UTR ?Gene //Added by Chris

WS227

*Summary //now only contains concise genomic description of the transgene in brackets
*Rescue XREF ?Variation// no XREF to ?Gene
Remove tags:
*Supporting_data //removed along with 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 tags:
*Promoter -> new tag for subtags Driven_by_gene and Driven_by_construct
*Reporter -> new tag to group Reporter_product and Gene
*Reporter_type -> new tag for Transcriptional fusion, Translational fusion 
*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
*Integrated -> new subtag and groups the mapping tags 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
 
For Map class
 ?Map
  Transgene  ?Transgene XREF Map
  Transgene  ?Transgene //sdm added to display gmaps //removed XREF ky 2011
  -D XREF Map

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\\