Difference between revisions of "WormBase Model:Transgene"
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==Approved Changes== | ==Approved Changes== | ||
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| + | ===WS238=== | ||
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| + | 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 | ||
| + | </pre> | ||
| + | ===WS237=== | ||
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| + | 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 | ||
| + | </pre> | ||
| + | ===WS234=== | ||
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| + | 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. | ||
| + | </pre> | ||
| + | ===WS233=== | ||
| + | Reporter 3_UTR ?Gene //Added by Chris | ||
===WS227=== | ===WS227=== | ||
| − | *Summary | + | <pre style="white-space: pre-wrap; |
| − | *Rescue | + | white-space: -moz-pre-wrap; |
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| + | *Summary //now only contains concise genomic description of the transgene in brackets | ||
| + | *Rescue XREF ?Variation// no XREF to ?Gene | ||
Remove tags: | Remove tags: | ||
| − | *Supporting_data | + | *Supporting_data //removed along with subtags |
*Isolation | *Isolation | ||
*Gamma_ray | *Gamma_ray | ||
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*Other_reporter | *Other_reporter | ||
| − | New | + | New tags: |
| − | *Promoter -> new tag for subtags Driven_by_gene and Driven_by_construct | + | *Promoter -> new tag for subtags Driven_by_gene and Driven_by_construct |
| − | *Reporter -> new tag to group Reporter_product and Gene | + | *Reporter -> new tag to group Reporter_product and Gene |
| − | *Reporter_type -> new tag for Transcriptional fusion, Translational fusion | + | *Reporter_type -> new tag for Transcriptional fusion, Translational fusion |
| − | *Construction -> new tag to group subtags | + | *Construction -> new tag to group subtags Fragment, Coinjection_marker, Integration_method |
*Genetic_information -> new tag to group new subtags Extrachromosomal and Integrated | *Genetic_information -> new tag to group new subtags Extrachromosomal and Integrated | ||
| − | *Extrachromosomal -> new subtag | + | *Extrachromosomal -> new subtag |
| − | *Integrated -> new subtag and groups the mapping tags | + | *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, | *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 | + | *Associated_with -> new tag to group subtags Marked_rearrangement, Clone, Strain |
Tag name changes | Tag name changes | ||
*Integration_method -> changed from Integrated_by | *Integration_method -> changed from Integrated_by | ||
| − | *Laboratory -> changed from Location | + | *Laboratory -> changed from Location |
For Map class | For Map class | ||
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?Map | ?Map | ||
Transgene ?Transgene XREF Map | Transgene ?Transgene XREF Map | ||
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-D XREF Map | -D XREF Map | ||
</pre> | </pre> | ||
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==Unused tags== | ==Unused tags== | ||
Revision as of 20:14, 4 October 2013
Contents
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
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\\
