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 | + | 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 | + | 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 | + | 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 | + | Reference ?Paper XREF Transgene // papers refered to the transgene. |
− | Species UNIQUE ?Species | + | Species UNIQUE ?Species // added by krb for consistency with other classes 021030 |
− | Remark ?Text #Evidence | + | 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
Contents
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