WS250 Models.wrm

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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


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


?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