Difference between revisions of "WormBase Model:Feature"

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(Updated for WS245 elegans data)
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== Unused tags ==
== Unused tags ==
Public_name - This will be good for UTRome data/modENCODE data that has a "real" name on the modENCODE pages?
Defined_by_author - ?
Defined_by_author - ?

Revision as of 08:37, 16 September 2014

WormBase Models

Curator Comments/Description


// Feature class

?Feature SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Feature_object
         Name Public_name UNIQUE ?Text
              Other_name ?Text
         Flanking_sequences UNIQUE ?Sequence UNIQUE Text UNIQUE Text
         DNA_text UNIQUE ?Text       // for storing the sequence of the feature...can use IUPAC codes to be able
                                     // store consensus sequences, e.g. binding site consensus sequence
         Origin     Species UNIQUE ?Species  //added by pad, as we are moving towards multi species readyness.
         History    Merged_into    UNIQUE    ?Feature XREF Acquires_merge #Evidence
                    Acquires_merge ?Feature XREF Merged_into #Evidence
                    Deprecated     Text      #Evidence 
         Visible    Description ?Text
                    SO_term ?SO_term XREF Feature
         Defined_by Defined_by_sequence ?Sequence XREF Defines_feature #Evidence
                    Defined_by_paper    ?Paper XREF Feature #Evidence
                    Defined_by_person   ?Person
                    Defined_by_author   ?Author
                    Defined_by_analysis ?Analysis 
         Associations Associated_with_gene       ?Gene       XREF Associated_feature #Evidence // richard
                      Associated_with_CDS        ?CDS        XREF Associated_feature #Evidence  // richard
                      Associated_with_transcript ?Transcript XREF Associated_feature #Evidence  // richard
                      Associated_with_pseudogene ?Pseudogene XREF Associated_feature #Evidence // richard
                      Associated_with_transposon ?Transposon XREF Associated_feature #Evidence //richard
                      Associated_with_variation  ?Variation  XREF Feature #Evidence  
                      Associated_with_Position_Matrix         ?Position_Matrix XREF Associated_feature #Evidence
                      Associated_with_operon      ?Operon XREF Associated_feature #Evidence
                      Associated_with_Interaction      ?Interaction XREF Associated_feature #Evidence
                      Associated_with_expression_pattern         ?Expr_pattern XREF Associated_feature #Evidence 
                      Associated_with_Feature ?Feature XREF Associated_with_Feature #Evidence 
         Bound_by_product_of ?Gene XREF Gene_product_binds #Evidence //pad added this to show what gene it binds
         Annotation UNIQUE ?LongText            // added for data attribution [030220 dl]
         Confidential_remark ?Text //pad
         Remark ?Text #Evidence
         Method UNIQUE ?Method

Proposed Changes

Unused tags

Defined_by_author - ?




Associated_with_Position_Matrix - unused and poss defunct? better connect the ?PM to the query substrate?