Difference between revisions of "WormBase Model:Feature"
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== Curator Comments/Description == | == Curator Comments/Description == | ||
+ | Updated model and unused tags for WS245 elegans data from pre-merged BUILD/elegans database. | ||
+ | == Model == | ||
+ | <pre> | ||
+ | /////////////////////////////////////////////////////////////////////////// | ||
+ | // | ||
+ | // 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 | ||
− | |||
− | |||
− | |||
</pre> | </pre> | ||
== Proposed Changes == | == 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 |
Latest revision as of 08:39, 16 September 2014
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