Difference between revisions of "WormBase Model:Transgene"
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/////////////////////////////////////////////////////////////////////////////// | /////////////////////////////////////////////////////////////////////////////// | ||
− | ?Transgene Summary UNIQUE ?Text // | + | ?Transgene Summary UNIQUE ?Text //concise genomic description of the transgene |
− | Synonym ?Text //for alternative names | + | Synonym ?Text //for alternative names |
− | + | Promoter Driven_by_gene ?Gene XREF Drives_transgene //eventually change this tag to promoter_gene | |
− | Driven_by_construct ?Text // | + | Driven_by_construct ?Text //eventually change this tag to promoter_artificial |
− | Reporter_product | + | Reporter Reporter_product ?Text //removed multiple tags for Reporter_product |
− | Gene ?Gene XREF Transgene_product Text | + | Gene ?Gene XREF Transgene_product Text |
− | + | Reporter_type ?Text // added for Transcriptional fusion or Translational fusion | |
− | Construction | + | Construction //new tag to collect the following as subtags |
− | Fragment Text ?Text // | + | 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 // | + | Author ?Author // may eventually be deleted |
− | Genetic_information | + | 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 | |
− | Phenotype ?Phenotype XREF Transgene #Phenotype_info | + | Map_evidence #Evidence |
− | Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info | + | Mapping_data 2_point ?2_point_data //if no data, can be removed |
− | Used_for Rescue | + | Multi_point ?Multi_pt_data //if no data can be removed |
− | Expr_pattern ?Expr_pattern XREF Transgene | + | Phenotype ?Phenotype XREF Transgene #Phenotype_info |
− | Marker_for ?Text #Evidence | + | Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info |
− | Gene_regulation ?Gene_regulation XREF Transgene | + | Used_for Rescue //new tag to collect the following as subtags |
− | Interactor ?Interaction // | + | ?Variation XREF Rescued_by_Transgene //removed ?Gene XREF Rescued_by_transgene |
− | + | Expr_pattern ?Expr_pattern XREF Transgene | |
− | + | Marker_for ?Text #Evidence | |
− | Clone ?Clone XREF Transgene Text | + | Gene_regulation ?Gene_regulation XREF Transgene |
− | Strain ?Strain XREF Transgene | + | Interactor ?Interaction |
− | Reference ?Paper XREF Transgene | + | Associated_with //new tag to collect the following as subtags |
− | Species UNIQUE ?Species | + | Marked_rearrangement ?Rearrangement XREF By_transgene |
− | Remark ?Text #Evidence | + | 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
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