WormBase Model:Transgene
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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 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
WS227
- 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)**
For Map class
?Map Transgene ?Transgene XREF Map Transgene ?Transgene //sdm added to display gmaps //removed XREF ky 2011 -D XREF Map
WS233
Reporter 3_UTR ?Gene //Added by Chris
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.
WS237
Construction_summary Text //To keep in sync with website tags - moved all Summary infor to Construction Summary, reorganize Summary tag for transgene genotype.
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\\