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
+
?Expr_pattern  Expression_of  Gene ?Gene XREF Expr_pattern //For genes that were studied
                                 CDS        ?CDS XREF Expr_pattern // for coding genes
+
                                 CDS        ?CDS XREF Expr_pattern //this tag is not used any more
                                 Sequence  ?Sequence XREF Expr_pattern // for clones???
+
                                 Sequence  ?Sequence XREF Expr_pattern //this tag is not used any more
                                 Pseudogene ?Pseudogene XREF Expr_pattern // [030801 krb]
+
                                 Pseudogene ?Pseudogene XREF Expr_pattern //this tag is not used any more
                                 Clone ?Clone XREF Expr_pattern
+
                                 Clone ?Clone XREF Expr_pattern //this is to record plasmid names for the study, not used any more
                                 Protein ?Protein XREF Expr_pattern
+
                                 Protein ?Protein XREF Expr_pattern //this tag is not used any more
                                 Protein_description Text  // stores information for Expr_patterns with unknown antigens [031105 krb]
+
                                 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 [060427 ar2]
+
                 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
+
                 Expressed_in    Cell        ?Cell        XREF Expr_pattern #Qualifier //this tag is not used any more
                                 Cell_group  ?Cell_group  XREF Expr_pattern #Qualifier
+
                                 Cell_group  ?Cell_group  XREF Expr_pattern #Qualifier //this tag is not used any more
                                 Life_stage  ?Life_stage  XREF Expr_pattern #Qualifier
+
                                 Life_stage  ?Life_stage  XREF Expr_pattern #Qualifier //expressed in life stages
                                 Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier
+
                                 Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier //expressed in tissue parts or cells
                                 GO_term      ?GO_term      XREF Expr_pattern #GR_condition
+
                                 GO_term      ?GO_term      XREF Expr_pattern #GR_condition //for cellular components
                 Subcellular_localization ?Text
+
                 Subcellular_localization ?Text //description on subcellular localization
                 Type    Reporter_gene ?Text
+
                 Type    Reporter_gene ?Text //The following tags indicate what kind of experiments were done.
 
                         In_situ Text
 
                         In_situ Text
 
                         Antibody ?Text
 
                         Antibody ?Text
                         Northern Text // Wen [krb 030425]
+
                         Northern Text
                         Western Text // Wen
+
                         Western Text  
                         RT_PCR Text   // Wen
+
                         RT_PCR Text
                         Localizome ?Text //added by Wen
+
                         Localizome ?Text
                 Expression_cluster ?Expression_cluster XREF Expr_pattern //added by Wen.for localizome
+
                 Expression_cluster ?Expression_cluster XREF Expr_pattern //For localizome data to summarize genes with similar expression profiles.
                 Pattern ?Text
+
                 Pattern ?Text //description of cellular and/or developmental expression pattern
                 Picture ?Picture XREF Expr_pattern
+
                 Picture ?Picture XREF Expr_pattern //link to picture files in WormBase.
                 MovieURL Text //Added by wen for link to movie URLs.
+
                 MovieURL Text //link to movie URLs that store movies externally
                 Movie    ?Movie    XREF Expr_pattern  //Added by Wen to curate Expr_pattern video
+
                 Movie    ?Movie    XREF Expr_pattern  //link to movie files in WormBase.
                 Remark ?Text #Evidence
+
                 Remark ?Text #Evidence //for any other information not fitting the model but still important.
                 Experiment      Laboratory ?Laboratory
+
                 Experiment      Laboratory ?Laboratory //Labs who performed the experiment. The following subtags are for data submitted by authors but not published.
                                 Author ?Author  
+
                                 Author ?Author //Author of the experiment
                                 Date UNIQUE DateType
+
                                 Date UNIQUE DateType //Date the experiment were performed or data submitted.
                                 Strain UNIQUE ?Strain
+
                                 Strain UNIQUE ?Strain //Stains used for the experiment
                 Reference ?Paper XREF Expr_pattern
+
                 Reference ?Paper XREF Expr_pattern //Paper that the experiments were published.
                 Transgene ?Transgene XREF Expr_pattern
+
                 Transgene ?Transgene XREF Expr_pattern //Transgene reagent used.
 
                 Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence
 
                 Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence
                 Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining
+
                 Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining, antibody reagent.
                                                          // added [031120 krb]
+
                 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.
                 Curated_by UNIQUE Text // Hinxton (HX) or Caltech (CIT) Sylvia [010927 krb]
 
 
 
 
</pre>
 
</pre>
  

Revision as of 22:39, 6 December 2010

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

Cell_group

GO_term

Expression_cluster

Movie