WormBase Model:Phenotype info

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WormBase Models

Curator Comments/Description

Usage hard to work out as tag counts don't work in hashes.


Model

////////////////////////////////////////////
//
// ?Phenotype_info Class
//
////////////////////////////////////////////

#Phenotype_info         Paper_evidence ?Paper
                        Person_evidence ?Person
                        Curator_confirmed       ?Person
                        Remark  ?Text   #Evidence // specific remarks about the phenotype
                        Quantity_description ?Text #Evidence //Remark to describe what quantity describes, below
                        Quantity        UNIQUE  Int UNIQUE      Int     #Evidence
                        Not             #Evidence //This is being phased out but is needed for the next phase [06/08/10].
                        Anatomy_term    ?Anatomy_term #Evidence 
                        Penetrance              Incomplete      Text    #Evidence
                                                Low             Text    #Evidence
                                                High            Text    #Evidence
                                                Complete        Text    #Evidence
                                                Range UNIQUE Int UNIQUE Int #Evidence // Range of penetrance
                        Recessive               #Evidence
                        Semi_dominant           #Evidence
                        Dominant                #Evidence
                        Haplo_insufficient      #Evidence
                        Caused_by ?Gene #Evidence
                        Caused_by_other ?Text #Evidence
                        Loss_of_function  UNIQUE        Hypomorph                               #Evidence
                                                        Amorph                                  #Evidence
                                                        Uncharacterised_loss_of_function        #Evidence
                        Gain_of_function  UNIQUE        Dominant_negative       #Evidence
                                                        Hypermorph              #Evidence
                                                        Neomorph                #Evidence
                                                        Uncharacterised_gain_of_function        #Evidence
                        Other_allele_type UNIQUE  Wild_type     #Evidence
                                                  Isoallele     #Evidence  
                                                  Mixed         #Evidence       
                        Affected_by     Molecule    ?Molecule    #Evidence // ?Molecule model Karen Yook
                        Temperature_sensitive   Heat_sensitive  Text            #Evidence
                                                Cold_sensitive  Text            #Evidence
                        Maternal        UNIQUE  Strictly_maternal       #Evidence
                                                With_maternal_effect    #Evidence
                        Paternal        #Evidence
                        Phenotype_assay Life_stage  ?Life_stage  #Evidence
                                        Strain      ?Strain      #Evidence
                                        Treatment   ?Text        #Evidence
                                        Temperature ?Text        #Evidence
                                        Genotype    ?Text        #Evidence 

Proposed Changes

unused tags

Approved Changes

WS231

Rescued_by_transgene ?Transgene//added
Ease_of_scoring  UNIQUE ES0_Impossible_to_score
                                     ES1_Very_hard_to_score
                                     ES2_Difficult_to_score
                                     ES3_Easy_to_score

WS219

?Phenotype //added by Wen for Not observed phenotypes

           Not_in_RNAi ?RNAi XREF Phenotype_not_observed
           Not_in_Variation ?Variation XREF Phenotype_not_observed
           Not_in_Strain ?Strain XREF Phenotype_not_observed
           Not_in_Transgene ?Transgene XREF Phenotype_not_observed
           Not_in_Rearrangement ?Rearrangement XREF Phenotype_not_observed


XREFs from ?Phenotype above ?RNAi, ?Variation, ?Strain, ?Transgene, ?Rearrangement

           Phenotype_not_observed ?Phenotype XREF Not_in_Rearrangement #Phenotype_info
           Phenotype_not_observed ?Phenotype XREF Not_in_Strain #Phenotype_info
           Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info
           Phenotype_not_observed ?Phenotype XREF Not_in_RNAi #Phenotype_info
           Phenotype_not_observed ?Phenotype XREF Not_in_Variation #Phenotype_info