WormBase Model:Expr pattern

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WormBase Models

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.