Difference between revisions of "WormBase Model:Feature"

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(Created page with '__TOC__ WormBase Models == Curator Comments/Description == == Model == <pre> </pre> == Proposed Changes ==')
 
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== Model ==
 
== Model ==
 
<pre>
 
<pre>
 +
///////////////////////////////////////////////////////////////////////////
 +
//
 +
// Feature class
 +
//
 +
///////////////////////////////////////////////////////////////////////////
 +
 +
?Feature SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Feature_object
 +
        Name Public_name UNIQUE ?Text
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              Other_name ?Text
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        Flanking_sequences UNIQUE ?Sequence UNIQUE Text UNIQUE Text
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        DNA_text UNIQUE ?Text      // for storing the sequence of the feature...can use IUPAC codes to be able
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                                    // 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
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                    Deprecated    Text      #Evidence
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        Visible    Description ?Text
 +
                    SO_term ?SO_term XREF Feature
 +
        Defined_by Defined_by_sequence ?Sequence XREF Defines_feature #Evidence
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                    Defined_by_paper    ?Paper XREF Feature #Evidence
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                    Defined_by_person  ?Person
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                    Defined_by_author  ?Author
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                    Defined_by_analysis ?Analysis
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        Associations Associated_with_gene      ?Gene      XREF Associated_feature #Evidence // richard
 +
                      Associated_with_CDS        ?CDS        XREF Associated_feature #Evidence  // richard
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                      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
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                      Associated_with_variation  ?Variation  XREF Feature #Evidence 
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                      Associated_with_Position_Matrix        ?Position_Matrix XREF Associated_feature #Evidence
 +
                      Associated_with_operon      ?Operon XREF Associated_feature #Evidence
 +
                      Associated_with_gene_regulation      ?Gene_regulation 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
  
 
</pre>
 
</pre>
  
 
== Proposed Changes ==
 
== Proposed Changes ==

Revision as of 10:28, 4 October 2010

WormBase Models

Curator Comments/Description

Model

///////////////////////////////////////////////////////////////////////////
//
// 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_gene_regulation      ?Gene_regulation 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