Difference between revisions of "Expression pattern remodel"

From WormBaseWiki
Jump to navigationJump to search
Line 118: Line 118:
 
</pre>
 
</pre>
  
−
==simplified summary of the changes==
+
==simplified summary of the changes for WS244==
 
   
 
   
  
Line 140: Line 140:
 
                 Present //for quantitative expression
 
                 Present //for quantitative expression
 
                 Absent  //for quantitative expression
 
                 Absent  //for quantitative expression
 +
 +
 +
===model of the future (WS2XX??)===
 +
 +
This will be the final version once all legacy objects will be remodeled accordingly.
 +
<pre>
 +
?Expr_pattern Expression_of Gene ?Gene XREF Expr_pattern #Evidence
 +
Clone ?Clone XREF Expr_pattern
 +
                                Protein_description Text  // stores information for Expr_patterns with unknown antigens [031105 krb]
 +
Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping [060427 ar2]
 +
                Detected_in ?Anatomy_term ?Life_stage ?GO_term ?float #Qualifier //added for quantitative/qualitative expression
 +
                Algorithm    ?Text //for quantitative expression
 +
                Subcellular_localization ?Text
 +
Type Reporter_gene ?Text
 +
In_situ Text
 +
Antibody ?Text
 +
Northern Text // Wen [krb 030425]
 +
                        Western Text  // Wen
 +
                        RT_PCR Text  // Wen
 +
Localizome ?Text //added by Wen
 +
Microarray ?Microarray_experiment
 +
Tiling_array ?Analysis
 +
EPIC   ?Text
 +
Expression_cluster ?Expression_cluster XREF Expr_pattern //added by Wen.for localizome
 +
Pattern ?Text
 +
Picture ?Picture XREF Expr_pattern
 +
MovieURL Text //Added by wen for link to movie URLs.
 +
Movie    ?Movie    XREF Expr_pattern  //Added by Wen to curate Expr_pattern video
 +
                Remark ?Text #Evidence
 +
DB_info ?Database ?Database_field Text
 +
                Experiment Laboratory ?Laboratory
 +
Author ?Author
 +
Date UNIQUE DateType
 +
Strain UNIQUE ?Strain
 +
Reference ?Paper XREF Expr_pattern
 +
                Transgene ?Transgene XREF Expr_pattern
 +
Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence
 +
Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining
 +
                                                          // added [031120 krb]
 +
Curated_by UNIQUE Text // Hinxton (HX) or Caltech (CIT) Sylvia [010927 krb]
 +
Historical_gene  ?Gene #Evidence
 +
 +
                                                                                               
 +
#Qualifier Certain  Text
 +
          Uncertain Text    //For faint or variable expression
 +
          Partial  Text    //For expression of unidentified cell in a cell group
 +
          Present //for quantitative expression
 +
          Absent  //for quantitative expression
 +
</pre>
 +
 +
==simplified summary of the changes for WS2XXX==
 +
removed
 +
                  Expressed_in Life_stage  ?Life_stage  XREF Expr_pattern #Qualifier
 +
Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier
 +
GO_term      ?GO_term      XREF Expr_pattern #GR_condition

Revision as of 12:44, 25 April 2014

This is a proposal for changing the current ?Expr_pattern model in order to capture

  • quantitative expression
  • life_stage, cellular_compartment expression specificity

we will also take the opportunity to clean up some unused tags

  • CDS: no objects‬
  • ‪ Sequence: 8 objects I could consolidate with other classes -e.g. clone‬
  • Pseudogene: no objects
  • Protein: 1 object, found by Paul D should figure out where it comes from
  • Cell: no objects
  • Cell_group: no objects

Current model (WS242)

?Expr_pattern	Expression_of	Gene ?Gene XREF Expr_pattern #Evidence
				CDS        ?CDS XREF Expr_pattern // for coding genes
				Sequence   ?Sequence XREF Expr_pattern // for clones???
				Pseudogene ?Pseudogene XREF Expr_pattern // [030801 krb]
				Clone ?Clone XREF Expr_pattern
				Protein ?Protein XREF Expr_pattern
                                Protein_description Text   // stores information for Expr_patterns with unknown antigens [031105 krb]
		Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping [060427 ar2]
		Expressed_in	Cell         ?Cell         XREF Expr_pattern #Qualifier
				Cell_group   ?Cell_group   XREF Expr_pattern #Qualifier
				Life_stage   ?Life_stage   XREF Expr_pattern #Qualifier
				Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier
				GO_term      ?GO_term      XREF Expr_pattern #GR_condition
                Subcellular_localization ?Text
		Type	Reporter_gene ?Text
			In_situ Text
			Antibody ?Text
			Northern Text // Wen [krb 030425]
                        Western Text  // Wen 
                        RT_PCR Text   // Wen
			Localizome ?Text //added by Wen
			Microarray ?Microarray_experiment
			Tiling_array ?Analysis
			EPIC	  ?Text 
		Expression_cluster ?Expression_cluster XREF Expr_pattern //added by Wen.for localizome
		Pattern ?Text
		Picture ?Picture XREF Expr_pattern
		MovieURL Text //Added by wen for link to movie URLs. 
		Movie    ?Movie    XREF Expr_pattern  //Added by Wen to curate Expr_pattern video
                Remark ?Text #Evidence
		DB_info ?Database ?Database_field Text
                Experiment	Laboratory ?Laboratory
				Author ?Author 
				Date UNIQUE DateType
				Strain UNIQUE ?Strain
		Reference ?Paper XREF Expr_pattern
                Transgene ?Transgene XREF Expr_pattern
		Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence
		Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining
                                                          // added [031120 krb]
		Curated_by UNIQUE Text // Hinxton (HX) or Caltech (CIT) Sylvia [010927 krb]
		Historical_gene   ?Gene #Evidence


//Qualifer hash will be used for Expr_pattern curation to specify the reliability of data.
                                                                                                 
#Qualifier Certain   Text
           Uncertain Text    //For faint or variable expression
           Partial   Text    //For expression of unidentified cell in a cell group

Proposed model (WS244?)

This is an ntermediate version until all legacy objects will be remodeled accordingly. In this version of the model the 2 scenarios will coexist: 

?Expr_pattern	Expression_of	Gene ?Gene XREF Expr_pattern #Evidence
				Clone ?Clone XREF Expr_pattern
                                Protein_description Text   // stores information for Expr_patterns with unknown antigens [031105 krb]
		Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping [060427 ar2]
                Detected_in ?Anatomy_term ?Life_stage ?GO_term ?float #Qualifier //added for quantitative/qualitative expression
                Algorithm    ?Text //for quantitative expression
		Expressed_in	Life_stage   ?Life_stage   XREF Expr_pattern #Qualifier
				Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier
				GO_term      ?GO_term      XREF Expr_pattern #GR_condition
                Subcellular_localization ?Text
		Type	Reporter_gene ?Text
			In_situ Text
			Antibody ?Text
			Northern Text // Wen [krb 030425]
                        Western Text  // Wen 
                        RT_PCR Text   // Wen
			Localizome ?Text //added by Wen
			Microarray ?Microarray_experiment
			Tiling_array ?Analysis
			EPIC	  ?Text 
		Expression_cluster ?Expression_cluster XREF Expr_pattern //added by Wen.for localizome
		Pattern ?Text
		Picture ?Picture XREF Expr_pattern
		MovieURL Text //Added by wen for link to movie URLs. 
		Movie    ?Movie    XREF Expr_pattern  //Added by Wen to curate Expr_pattern video
                Remark ?Text #Evidence
		DB_info ?Database ?Database_field Text
                Experiment	Laboratory ?Laboratory
				Author ?Author 
				Date UNIQUE DateType
				Strain UNIQUE ?Strain
		Reference ?Paper XREF Expr_pattern
                Transgene ?Transgene XREF Expr_pattern
		Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence
		Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining
                                                          // added [031120 krb]
		Curated_by UNIQUE Text // Hinxton (HX) or Caltech (CIT) Sylvia [010927 krb]
		Historical_gene   ?Gene #Evidence

                                                                                                 
#Qualifier Certain   Text
           Uncertain Text    //For faint or variable expression
           Partial   Text    //For expression of unidentified cell in a cell group
           Present //for quantitative expression
           Absent  //for quantitative expression

simplified summary of the changes for WS244


removed
                                CDS        ?CDS XREF Expr_pattern // for coding genes
				Sequence   ?Sequence XREF Expr_pattern // for clones???
				Pseudogene ?Pseudogene XREF Expr_pattern // [030801 krb]
				Protein ?Protein XREF Expr_pattern

                                Cell         ?Cell         XREF Expr_pattern #Qualifier
				Cell_group   ?Cell_group   XREF Expr_pattern #Qualifier

added

                        Detected_in ?Anatomy_term ?Life_stage ?GO_term ?float #Qualifier //added for quantitative/qualitative expression
                        Algorithm    ?Text //for quantitative expression

#Qualifier  ...
                Present //for quantitative expression
                Absent  //for quantitative expression


===model of the future (WS2XX??)===

This will be the final version once all legacy objects will be remodeled accordingly. 
<pre>
?Expr_pattern	Expression_of	Gene ?Gene XREF Expr_pattern #Evidence
				Clone ?Clone XREF Expr_pattern
                                Protein_description Text   // stores information for Expr_patterns with unknown antigens [031105 krb]
		Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping [060427 ar2]
                Detected_in ?Anatomy_term ?Life_stage ?GO_term ?float #Qualifier //added for quantitative/qualitative expression
                Algorithm    ?Text //for quantitative expression
                Subcellular_localization ?Text
		Type	Reporter_gene ?Text
			In_situ Text
			Antibody ?Text
			Northern Text // Wen [krb 030425]
                        Western Text  // Wen 
                        RT_PCR Text   // Wen
			Localizome ?Text //added by Wen
			Microarray ?Microarray_experiment
			Tiling_array ?Analysis
			EPIC	  ?Text 
		Expression_cluster ?Expression_cluster XREF Expr_pattern //added by Wen.for localizome
		Pattern ?Text
		Picture ?Picture XREF Expr_pattern
		MovieURL Text //Added by wen for link to movie URLs. 
		Movie    ?Movie    XREF Expr_pattern  //Added by Wen to curate Expr_pattern video
                Remark ?Text #Evidence
		DB_info ?Database ?Database_field Text
                Experiment	Laboratory ?Laboratory
				Author ?Author 
				Date UNIQUE DateType
				Strain UNIQUE ?Strain
		Reference ?Paper XREF Expr_pattern
                Transgene ?Transgene XREF Expr_pattern
		Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence
		Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining
                                                          // added [031120 krb]
		Curated_by UNIQUE Text // Hinxton (HX) or Caltech (CIT) Sylvia [010927 krb]
		Historical_gene   ?Gene #Evidence

                                                                                                 
#Qualifier Certain   Text
           Uncertain Text    //For faint or variable expression
           Partial   Text    //For expression of unidentified cell in a cell group
           Present //for quantitative expression
           Absent  //for quantitative expression

simplified summary of the changes for WS2XXX

removed 

                  Expressed_in	Life_stage   ?Life_stage   XREF Expr_pattern #Qualifier

Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier GO_term ?GO_term XREF Expr_pattern #GR_condition

Retrieved from "https://wiki.wormbase.org/index.php?title=Expression_pattern_remodel&oldid=23007"