Difference between revisions of "WS250 Models.wrm"

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GO_term Model change
+
====GO_term Model change====
--------------------
+
 
  
 
1) Remove the Term tag.  The name of the GO_term would be populated in the
 
1) Remove the Term tag.  The name of the GO_term would be populated in the
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GO_annotation mods
+
====GO_annotation mods====
------------------
+
 
 
Thomas input suggests: UNIQUE for single value (most notable Gene, GO_Term, and GO_Code)
 
Thomas input suggests: UNIQUE for single value (most notable Gene, GO_Term, and GO_Code)
 
Kimberly: I agree that we could add UNIQUE constraints to Gene, GO_term, and
 
Kimberly: I agree that we could add UNIQUE constraints to Gene, GO_term, and
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Request for phenotype_info tag name changes
+
====Request for phenotype_info tag name changes====
-------------------------------------------
 
  
Variation_effect Gain_of_function_undetermined_type    #Evidence
+
 
 +
Variation_effect Gain_of_function_undetermined_type    #Evidence
 
Antimorph_gain_of_function    #Evidence
 
Antimorph_gain_of_function    #Evidence
 
Dominant_negative_gain_of_function    #Evidence
 
Dominant_negative_gain_of_function    #Evidence
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Wild_allele    #Evidence
 
Wild_allele    #Evidence
  
Expr_pattern model change
+
====Expr_pattern model change====
-------------------------
+
 
  
 
Remove Cell and Cell_group
 
Remove Cell and Cell_group
  
Expression_data Life_stage ?Life_stage XREF Expr_pattern #Qualifier
+
Expression_data Life_stage ?Life_stage XREF Expr_pattern #Qualifier
                Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier
+
                Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier
                GO_term ?GO_term XREF Expr_pattern #GR_condition
+
                GO_term ?GO_term XREF Expr_pattern #GR_condition
                Not_in_Life_stage ?Life_stage #Qualifier
+
                Not_in_Life_stage ?Life_stage #Qualifier
                Not_in_Anatomy_term ?Anatomy_term #Qualifier
+
                Not_in_Anatomy_term ?Anatomy_term #Qualifier
                Not_in_GO_term ?GO_term #GR_condition  
+
                Not_in_GO_term ?GO_term #GR_condition  
  
  
WBProcess class
+
====WBProcess class====
---------------
 
  
?WBProcess      Public_name UNIQUE ?Text
+
 
                Summary UNIQUE ?Text #Evidence
+
?WBProcess      Public_name UNIQUE ?Text
                Other_name ?Text
+
                Summary UNIQUE ?Text #Evidence
                Related_topic ....
+
                Other_name ?Text
                // Everything else unchanged.
+
                Related_topic ....
 +
                // Everything else unchanged.
  
 
Name' is not needed.  
 
Name' is not needed.  
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Gene - Biotype
+
====Gene - Biotype====
--------------
+
 
 
?Gene Gene_info Biotype UNIQUE ?SO_term
 
?Gene Gene_info Biotype UNIQUE ?SO_term
  
  
 
UNIQUE Quest
 
 
====UNIQUE Quest====
 
====UNIQUE Quest====
  
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  ?Rearrangement Isolation Date DateType
 
  ?Rearrangement Isolation Date DateType
 
                                 Source_rearrangement ?Rearrangement
 
                                 Source_rearrangement ?Rearrangement
 
 
  
 
SO_term UNIQUE tags
 
SO_term UNIQUE tags
 
-------------------
 
-------------------
 
  SO_name and SO_definition should be UNIQUE
 
  SO_name and SO_definition should be UNIQUE

Latest revision as of 08:32, 22 June 2015

GO_term Model change

1) Remove the Term tag. The name of the GO_term would be populated in the Name tag. This change will have downstream effects for the build and web display.

2) Add an Alt_id tag to populate secondary IDs as listed in the GO obo file. This would allow anyone searching WB with a secondary, or alternate, GO ID to still arrive at the correct GO_term page.

3) Although this doesn't affect any tags in the model, starting with WS250 we will populate the Version tag with the information in the 'data-version:' tag in the obo file, not the 'remark' tag that holds the SVN revision number. All terms have the Version tag populated, so we should remove the comment in the ?GO_term model about version only being stored on the 3 parent terms.

4) Version Version UNIQUE Text UNIQUE Text // Lincoln, to store version number of GO

to

Version UNIQUE Text // store "Gene Ontology releases/2015-06-13" as single value.


GO_annotation mods

Thomas input suggests: UNIQUE for single value (most notable Gene, GO_Term, and GO_Code) Kimberly: I agree that we could add UNIQUE constraints to Gene, GO_term, and GO_code. We could probably also add the UNIQUE constraint to Reference and GO_reference as well as Contributed_by and Date_last_updated.



Request for phenotype_info tag name changes

Variation_effect 	Gain_of_function_undetermined_type    #Evidence

Antimorph_gain_of_function #Evidence Dominant_negative_gain_of_function #Evidence Hypermorph_gain_of_function #Evidence Neomorph_gain_of_function #Evidence Loss_of_function_undetermined_extent #Evidence Null #Evidence Predicted_null_via_sequence #Evidence Probable_null_via_phenotype #Evidence Hypomorph_reduction_of_function #Evidence Predicted_hypomorph_via_sequence #Evidence Probable_hypomorph_via_phenotype #Evidence Wild_allele #Evidence

Expr_pattern model change

Remove Cell and Cell_group

Expression_data 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
                Not_in_Life_stage ?Life_stage #Qualifier
                Not_in_Anatomy_term ?Anatomy_term #Qualifier
                Not_in_GO_term ?GO_term #GR_condition 


WBProcess class

?WBProcess      Public_name UNIQUE ?Text
                Summary UNIQUE ?Text #Evidence
                Other_name ?Text
                Related_topic ....
                // Everything else unchanged.

Name' is not needed.

Summary UNIQUE ?Text #Evidence in ?Construct and Remark in ?Phenotype_info (Remark should actually be Summary).

Yes, Process_term can be deleted.


Gene - Biotype

?Gene Gene_info Biotype UNIQUE ?SO_term


UNIQUE Quest

?Strain Genotype Text
               Properties Outcrossed Text
?Rearrangement Isolation Date DateType
                               Source_rearrangement ?Rearrangement

SO_term UNIQUE tags


SO_name and SO_definition should be UNIQUE