Difference between revisions of "WormBase Model:Transgene"
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== Curator Comments/Description == | == Curator Comments/Description == | ||
+ | ==Updated model for WS245== | ||
+ | <pre> | ||
+ | ?Transgene Evidence #Evidence | ||
+ | Public_name UNIQUE ?Text | ||
+ | Summary UNIQUE ?Text | ||
+ | Synonym ?Text | ||
+ | Corresponding_variation UNIQUE ?Variation XREF Corresponding_transgene //put in to unambiguously associate the allele/transgene | ||
+ | Construction Construct ?Construct XREF Transgene_construct | ||
+ | Coinjection ?Construct XREF Transgene_coinjection | ||
+ | Coinjection_other ?Text //for coinjection markers that are not specified as a construct | ||
+ | Integration_method UNIQUE ?Text | ||
+ | Integrated_from ?Transgene XREF Transgene_derivation | ||
+ | Laboratory ?Laboratory #Lab_Location | ||
+ | Author ?Author | ||
+ | Construction_summary ?Text | ||
+ | Genetic_information Extrachromosomal | ||
+ | Integrated | ||
+ | Map ?Map #Map_position //needed for transgenes with no granular mapping, e.g., just mapped to a LG | ||
+ | Mapping_data 2_point ?2_point_data //deleted for WS245, rolled back for WS246 | ||
+ | Map_evidence #Evidence | ||
+ | Phenotype ?Phenotype XREF Transgene #Phenotype_info | ||
+ | Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info | ||
+ | Used_for Transgene_derivation ?Transgene XREF Integrated_from | ||
+ | Expr_pattern ?Expr_pattern XREF Transgene | ||
+ | Marker_for ?Text #Evidence | ||
+ | Interactor ?Interaction | ||
+ | Associated_with Marked_rearrangement ?Rearrangement XREF By_transgene | ||
+ | Strain ?Strain XREF Transgene | ||
+ | Reference ?Paper XREF Transgene | ||
+ | Species UNIQUE ?Species | ||
+ | Remark ?Text #Evidence | ||
+ | Historical_gene ?Gene #Evidence | ||
− | + | </pre> | |
− | + | ===Pre WS245 model=== | |
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<pre> | <pre> | ||
+ | ?Transgene Evidence #Evidence | ||
+ | Public_name //added for WS234 | ||
+ | Summary UNIQUE ?Text | ||
+ | Synonym ?Text | ||
+ | Promoter Driven_by_gene ?Gene XREF Drives_Transgene | ||
+ | Driven_by_construct ?Text | ||
+ | Reporter Reporter_product ?Text | ||
+ | Gene ?Gene XREF Transgene_product Text | ||
+ | 3_UTR ?Gene | ||
+ | Reporter_type ?Text | ||
+ | Construction Fragment ?Text | ||
+ | Coinjection_marker ?Text | ||
+ | Integration_method UNIQUE ?Text | ||
+ | Laboratory ?Laboratory #Lab_Location | ||
+ | Author ?Author | ||
+ | Person ?Person | ||
+ | Genetic_information Extrachromosomal | ||
+ | Integrated | ||
+ | Map ?Map #Map_position | ||
+ | Map_evidence #Evidence | ||
+ | Mapping_data 2_point ?2_point_data | ||
+ | Multi_point ?Multi_pt_data | ||
+ | Phenotype ?Phenotype XREF Transgene #Phenotype_info | ||
+ | Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info | ||
+ | Used_for | ||
+ | Expr_pattern ?Expr_pattern XREF Transgene | ||
+ | Marker_for ?Text #Evidence | ||
+ | Gene_regulation ?Gene_regulation XREF Transgene | ||
+ | Interactor ?Interaction | ||
+ | Associated_with 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 | ||
+ | </pre> | ||
+ | --[[User:Kyook|kjy]] 00:16, 26 May 2012 (UTC) | ||
== Proposed Updated Model 03 March 2011== | == Proposed Updated Model 03 March 2011== | ||
− | + | <pre> | |
/////////////////////////////////////////////////////////////////////////////// | /////////////////////////////////////////////////////////////////////////////// | ||
//Proposed Transgene class 03/11 for WS227 | //Proposed Transgene class 03/11 for WS227 | ||
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Reporter Reporter_product ?Text //removed multiple tags for Reporter_product | Reporter Reporter_product ?Text //removed multiple tags for Reporter_product | ||
Gene ?Gene XREF Transgene_product Text | Gene ?Gene XREF Transgene_product Text | ||
+ | 3_UTR ?Gene | ||
Reporter_type ?Text // added for Transcriptional fusion or Translational fusion | Reporter_type ?Text // added for Transcriptional fusion or Translational fusion | ||
Construction //new tag to collect the following as subtags | Construction //new tag to collect the following as subtags | ||
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− | + | == Model 03 March 2011 pre-WS227== | |
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<pre> | <pre> | ||
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/////////////////////////////////////////////////////////////////////////////// | /////////////////////////////////////////////////////////////////////////////// | ||
//Transgene class from Wen Chen 12/00 | //Transgene class from Wen Chen 12/00 | ||
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==Approved Changes== | ==Approved Changes== | ||
+ | ===WS251=== | ||
+ | <pre> | ||
+ | Transgene_for_disease ?DO_term XREF Associated_transgene #Evidence | ||
+ | </pre> | ||
+ | ===WS238=== | ||
+ | <pre style="white-space: pre-wrap; | ||
+ | white-space: -moz-pre-wrap; | ||
+ | white-space: -pre-wrap; | ||
+ | white-space: -o-pre-wrap; | ||
+ | word-wrap: break-word;"> | ||
+ | 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=== | ||
+ | <pre style="white-space: pre-wrap; | ||
+ | white-space: -moz-pre-wrap; | ||
+ | white-space: -pre-wrap; | ||
+ | white-space: -o-pre-wrap; | ||
+ | word-wrap: break-word;"> | ||
+ | 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=== | ||
+ | <pre style="white-space: pre-wrap; | ||
+ | white-space: -moz-pre-wrap; | ||
+ | white-space: -pre-wrap; | ||
+ | white-space: -o-pre-wrap; | ||
+ | word-wrap: break-word;"> | ||
+ | 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; |
− | + | white-space: -pre-wrap; | |
+ | white-space: -o-pre-wrap; | ||
+ | word-wrap: break-word;"> | ||
+ | *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== |
Latest revision as of 20:12, 22 September 2015
Contents
Curator Comments/Description
Updated model for WS245
?Transgene Evidence #Evidence Public_name UNIQUE ?Text Summary UNIQUE ?Text Synonym ?Text Corresponding_variation UNIQUE ?Variation XREF Corresponding_transgene //put in to unambiguously associate the allele/transgene Construction Construct ?Construct XREF Transgene_construct Coinjection ?Construct XREF Transgene_coinjection Coinjection_other ?Text //for coinjection markers that are not specified as a construct Integration_method UNIQUE ?Text Integrated_from ?Transgene XREF Transgene_derivation Laboratory ?Laboratory #Lab_Location Author ?Author Construction_summary ?Text Genetic_information Extrachromosomal Integrated Map ?Map #Map_position //needed for transgenes with no granular mapping, e.g., just mapped to a LG Mapping_data 2_point ?2_point_data //deleted for WS245, rolled back for WS246 Map_evidence #Evidence Phenotype ?Phenotype XREF Transgene #Phenotype_info Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info Used_for Transgene_derivation ?Transgene XREF Integrated_from Expr_pattern ?Expr_pattern XREF Transgene Marker_for ?Text #Evidence Interactor ?Interaction Associated_with Marked_rearrangement ?Rearrangement XREF By_transgene Strain ?Strain XREF Transgene Reference ?Paper XREF Transgene Species UNIQUE ?Species Remark ?Text #Evidence Historical_gene ?Gene #Evidence
Pre WS245 model
?Transgene Evidence #Evidence Public_name //added for WS234 Summary UNIQUE ?Text Synonym ?Text Promoter Driven_by_gene ?Gene XREF Drives_Transgene Driven_by_construct ?Text Reporter Reporter_product ?Text Gene ?Gene XREF Transgene_product Text 3_UTR ?Gene Reporter_type ?Text Construction Fragment ?Text Coinjection_marker ?Text Integration_method UNIQUE ?Text Laboratory ?Laboratory #Lab_Location Author ?Author Person ?Person Genetic_information Extrachromosomal Integrated Map ?Map #Map_position Map_evidence #Evidence Mapping_data 2_point ?2_point_data Multi_point ?Multi_pt_data Phenotype ?Phenotype XREF Transgene #Phenotype_info Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info Used_for Expr_pattern ?Expr_pattern XREF Transgene Marker_for ?Text #Evidence Gene_regulation ?Gene_regulation XREF Transgene Interactor ?Interaction Associated_with 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
--kjy 00:16, 26 May 2012 (UTC)
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 3_UTR ?Gene 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
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
WS251
Transgene_for_disease ?DO_term XREF Associated_transgene #Evidence
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\\