Difference between revisions of "WormBase Model:Expr pattern"
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== Model == | == Model == | ||
<pre> | <pre> | ||
− | + | ?Expr_pattern Expression_of Gene ?Gene XREF Expr_pattern //For genes that were studied | |
+ | CDS ?CDS XREF Expr_pattern //this tag is not used any more | ||
+ | Sequence ?Sequence XREF Expr_pattern //this tag is not used any more | ||
+ | Pseudogene ?Pseudogene XREF Expr_pattern //this tag is not used any more | ||
+ | Clone ?Clone XREF Expr_pattern //this is to record plasmid names for the study, not used any more | ||
+ | Protein ?Protein XREF Expr_pattern //this tag is not used any more | ||
+ | Protein_description Text // stores information for Expr_patterns done with immunostaining with unknown antigens | ||
+ | Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping | ||
+ | Expressed_in Cell ?Cell XREF Expr_pattern #Qualifier //this tag is not used any more | ||
+ | Cell_group ?Cell_group XREF Expr_pattern #Qualifier //this tag is not used any more | ||
+ | Life_stage ?Life_stage XREF Expr_pattern #Qualifier //expressed in life stages | ||
+ | Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier //expressed in tissue parts or cells | ||
+ | GO_term ?GO_term XREF Expr_pattern #GR_condition //for cellular components | ||
+ | Subcellular_localization ?Text //description on subcellular localization | ||
+ | Type Reporter_gene ?Text //The following tags indicate what kind of experiments were done. | ||
+ | In_situ Text | ||
+ | Antibody ?Text | ||
+ | Northern Text | ||
+ | Western Text | ||
+ | RT_PCR Text | ||
+ | Localizome ?Text | ||
+ | Expression_cluster ?Expression_cluster XREF Expr_pattern //For localizome data to summarize genes with similar expression profiles. | ||
+ | Pattern ?Text //description of cellular and/or developmental expression pattern | ||
+ | Picture ?Picture XREF Expr_pattern //link to picture files in WormBase. | ||
+ | MovieURL Text //link to movie URLs that store movies externally | ||
+ | Movie ?Movie XREF Expr_pattern //link to movie files in WormBase. | ||
+ | Remark ?Text #Evidence //for any other information not fitting the model but still important. | ||
+ | Experiment Laboratory ?Laboratory //Labs who performed the experiment. The following subtags are for data submitted by authors but not published. | ||
+ | Author ?Author //Author of the experiment | ||
+ | Date UNIQUE DateType //Date the experiment were performed or data submitted. | ||
+ | Strain UNIQUE ?Strain //Stains used for the experiment | ||
+ | Reference ?Paper XREF Expr_pattern //Paper that the experiments were published. | ||
+ | Transgene ?Transgene XREF Expr_pattern //Transgene reagent used. | ||
+ | Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence | ||
+ | Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining, antibody reagent. | ||
+ | Curated_by UNIQUE Text //To identify whether the curation was done by Hixton or Caltech. Not useful any more since all data are now curated by Caltech. | ||
</pre> | </pre> | ||
== Proposed Changes == | == Proposed Changes == | ||
+ | |||
+ | == unused tags == | ||
+ | |||
+ | CDS -- can be removed, replaced by Gene. | ||
+ | |||
+ | Sequence - can be removed, replaced by Gene. | ||
+ | |||
+ | Pseudogene - can be removed, replaced by Gene. | ||
+ | |||
+ | Protein - can be removed, replaced by Gene. | ||
+ | |||
+ | Cell -- can be removed, replaced by Anatomy_term | ||
+ | |||
+ | Cell_group -- can be removed, replaced by Anatomy_term | ||
+ | |||
+ | GO_term -- this is currently used extensively. | ||
+ | |||
+ | Expression_cluster -- used by localizome data | ||
+ | |||
+ | Movie -- not used although plan to use it in the future. |
Latest revision as of 22:42, 6 December 2010
Curator Comments/Description
Model
?Expr_pattern Expression_of Gene ?Gene XREF Expr_pattern //For genes that were studied CDS ?CDS XREF Expr_pattern //this tag is not used any more Sequence ?Sequence XREF Expr_pattern //this tag is not used any more Pseudogene ?Pseudogene XREF Expr_pattern //this tag is not used any more Clone ?Clone XREF Expr_pattern //this is to record plasmid names for the study, not used any more Protein ?Protein XREF Expr_pattern //this tag is not used any more Protein_description Text // stores information for Expr_patterns done with immunostaining with unknown antigens Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping Expressed_in Cell ?Cell XREF Expr_pattern #Qualifier //this tag is not used any more Cell_group ?Cell_group XREF Expr_pattern #Qualifier //this tag is not used any more Life_stage ?Life_stage XREF Expr_pattern #Qualifier //expressed in life stages Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier //expressed in tissue parts or cells GO_term ?GO_term XREF Expr_pattern #GR_condition //for cellular components Subcellular_localization ?Text //description on subcellular localization Type Reporter_gene ?Text //The following tags indicate what kind of experiments were done. In_situ Text Antibody ?Text Northern Text Western Text RT_PCR Text Localizome ?Text Expression_cluster ?Expression_cluster XREF Expr_pattern //For localizome data to summarize genes with similar expression profiles. Pattern ?Text //description of cellular and/or developmental expression pattern Picture ?Picture XREF Expr_pattern //link to picture files in WormBase. MovieURL Text //link to movie URLs that store movies externally Movie ?Movie XREF Expr_pattern //link to movie files in WormBase. Remark ?Text #Evidence //for any other information not fitting the model but still important. Experiment Laboratory ?Laboratory //Labs who performed the experiment. The following subtags are for data submitted by authors but not published. Author ?Author //Author of the experiment Date UNIQUE DateType //Date the experiment were performed or data submitted. Strain UNIQUE ?Strain //Stains used for the experiment Reference ?Paper XREF Expr_pattern //Paper that the experiments were published. Transgene ?Transgene XREF Expr_pattern //Transgene reagent used. Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining, antibody reagent. Curated_by UNIQUE Text //To identify whether the curation was done by Hixton or Caltech. Not useful any more since all data are now curated by Caltech.
Proposed Changes
unused tags
CDS -- can be removed, replaced by Gene.
Sequence - can be removed, replaced by Gene.
Pseudogene - can be removed, replaced by Gene.
Protein - can be removed, replaced by Gene.
Cell -- can be removed, replaced by Anatomy_term
Cell_group -- can be removed, replaced by Anatomy_term
GO_term -- this is currently used extensively.
Expression_cluster -- used by localizome data
Movie -- not used although plan to use it in the future.