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Transgene model
kyook edited this page Sep 5, 2012
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2 revisions
Public_name tag added. Transgenes will be assigned sequential WBTransgeneIDs 8-digits
?Transgene Summary UNIQUE ?Text //concise genomic description of the transgene
Synonym ?Text //for alternative names
Promoter //new tag for subtags
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 //collapsed tags for Reporter_product **(no change to .ace dumper)**
Gene ?Gene XREF Transgene_product Text
Reporter_type ?Text //new tag for Transcriptional fusion, Translational fusion **(need to add to .ace dumper and OA)**
Construction //new tag to group 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 **(change ace dumper and OA)**
Author ?Author // may eventually be deleted
Genetic_information //new tag to group the following as subtags
Extrachromosomal //new subtag **(change dumper and OA)**
Integrated //new subtag and group the mapping tags **(change dumper and OA)**
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 group the following as subtags
Rescue ?Variation XREF Rescued_by_Transgene //removed ?Gene XREF Rescued_by_transgene **(change dumper and OA)**
Expr_pattern ?Expr_pattern XREF Transgene
Marker_for ?Text #Evidence
Gene_regulation ?Gene_regulation XREF Transgene
Interactor ?Interaction
Associated_with //new tag to group 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
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 assay
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
- Summary** -> now only contains concise genomic description of the transgene in brackets\\
- Rescue** -> only XREF ?Variation, not ?Gene
- 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
- 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)**
- 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
- Integration_method -> changed from Integrated_by
- Laboratory -> changed from Location **(change ace dumper and OA)**
- 2_point -> if nothing in it, remove it
- Rescue -> changed use of tag, will be used
- Supporting_data -> remove
- Movie -> remove
- Picture -> remove