WormBase Model:Feature

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WormBase Models

Curator Comments/Description

Updated model and unused tags for WS245 elegans data from pre-merged BUILD/elegans database.

Model

///////////////////////////////////////////////////////////////////////////
//
// Feature class
//
///////////////////////////////////////////////////////////////////////////

?Feature SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Feature_object
         Name Public_name UNIQUE ?Text
              Other_name ?Text
         Sequence_details Flanking_sequences UNIQUE Text UNIQUE Text
                          Mapping_target UNIQUE ?Sequence 
                          Source_location UNIQUE Int UNIQUE ?Sequence UNIQUE Int UNIQUE Int UNIQUE #Evidence //source data, <WSversion> ?Sequence pos1 pos2 Evidence(Paper/person etc. remarks)
         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.
                    Strain UNIQUE ?Strain//added by pad, as we are moving towards multi strain 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
         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 Int
         Score Float Text #Evidence // this would be a log score as indicated by the analysis used in gff dump
         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 Feature_interactor
                      Associated_with_expression_pattern ?Expr_pattern XREF Associated_feature #Evidence 
                      Associated_with_Feature ?Feature XREF Associated_with_Feature #Evidence
                      Associated_with_construct ?Construct XREF Sequence_feature
         Bound_by_product_of ?Gene XREF Gene_product_binds #Evidence //pad added this to show what gene it binds
         Transcription_factor UNIQUE ?Transcription_factor XREF Binding_site 
         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_transposon

Associated_with_variation

Associated_with_construct

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

Annotation