WormBase Model:Gene

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WormBase Models

Curator Comments/Description

Model

////////////////////////////////////////////////////////////////////////////////////////
//
//  ?Gene class - krb
//
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?Gene   Evidence #Evidence
        SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Gene_child
        Identity  Version UNIQUE Int
                  Name  CGC_name        UNIQUE ?Gene_name XREF CGC_name_for #Evidence
                        Sequence_name   UNIQUE ?Gene_name XREF Sequence_name_for // captures main CDS name without isoforms
                        Molecular_name         ?Gene_name XREF Molecular_name_for  // for linking to full CDS names, wormpep etc.
                        Other_name             ?Gene_name XREF Other_name_for #Evidence // other unapproved CGC-style gene names
                        Public_name     UNIQUE ?Gene_name XREF Public_name_for // the one name that should be used
                  DB_info Database ?Database ?Database_field ?Accession_number //For Darin genbank genpep ids
                  Species UNIQUE ?Species
                  History Version_change Int UNIQUE DateType UNIQUE ?Person #Gene_history_action
                          Merged_into UNIQUE ?Gene XREF Acquires_merge
                          Acquires_merge ?Gene XREF Merged_into
                          Split_from UNIQUE ?Gene XREF Split_into
                          Split_into ?Gene XREF Split_from
                          Made_into_transposon
                  Status UNIQUE Live #Evidence
                                Suppressed #Evidence
                                Dead #Evidence   
        Gene_info Gene_class UNIQUE ?Gene_class XREF Genes
                  Laboratory ?Laboratory
                  Cloned_by #Evidence      // mt3 acreditation of person who cloned gene [060829 ar2]
                  Reference_allele ?Variation #Evidence
                  Allele ?Variation XREF Gene #Evidence
                  Possibly_affected_by ?Variation XREF Possibly_affects #Evidence
                  Legacy_information Text #Evidence
                  Complementation_data Text
                  Strain ?Strain XREF Gene
                  In_cluster ?Gene_cluster XREF Contains_gene // linking to Clusters in locus class
                  GO_term ?GO_term XREF Gene ?GO_code #Evidence
                  Contained_in_operon ?Operon XREF Contains_gene
                  Ortholog ?Gene XREF Ortholog ?Species #Evidence
                  Paralog ?Gene XREF Paralog ?Species #Evidence
                  Ortholog_other  ?Protein XREF Ortholog_gene #Evidence // to allow Orthologues links to none ?Gene genes eg remanei (ar2 Nov06)
                  Structured_description Provisional_description ?Text #Evidence         // Erich [020322 krb]
                                         Detailed_description ?Text #Evidence            // Erich [020322 krb]
                                         Concise_description ?Text #Evidence             // Erich [020523 krb]
                                         Other_description ?Text #Evidence               // Carol [050202 dl]
                                         Sequence_features ?Text #Evidence               // Carol [050202 dl]
                                         Functional_pathway ?Text #Evidence              // Carol [050202 dl]
                                         Functional_physical_interaction ?Text #Evidence // Carol [050202 dl]
                                         Biological_process ?Text #Evidence              // Carol [050202 dl]
                                         Molecular_function ?Text #Evidence              // Carol [050202 dl]
                                         Expression ?Text #Evidence                      // Carol [050202 dl]
        Molecular_info Corresponding_CDS ?CDS XREF Gene #Evidence             // to link to live CDSs
                       Corresponding_CDS_history ?CDS XREF Gene_history       // to link to history CDSs
                       Corresponding_transcript ?Transcript XREF Gene #Evidence
                       Corresponding_transcript_history ?Transcript XREF Gene_history
                       Corresponding_pseudogene ?Pseudogene XREF Gene #Evidence
                       Corresponding_pseudogene_history ?Pseudogene XREF Gene_history
                       Other_sequence ?Sequence XREF Gene #Evidence  // for linking to mRNAs etc. that correspond to a gene                
                       Associated_feature ?Feature XREF Associated_with_gene #Evidence
                       Gene_product_binds ?Feature XREF Bound_by_product_of
        Experimental_info RNAi_result ?RNAi XREF Gene #Evidence
                          Expr_pattern ?Expr_pattern XREF Gene
                          Drives_Transgene ?Transgene XREF Driven_by_gene
                          Transgene_product ?Transgene XREF Gene
                          Rescued_by_transgene ?Transgene
                          Gene_regulation Trans_regulator ?Gene_regulation XREF Trans_regulator_gene
                                          Trans_target    ?Gene_regulation XREF Trans_regulated_gene
                          Antibody ?Antibody XREF Gene
                          Microarray_results ?Microarray_results XREF Gene
                          Expression_cluster ?Expression_cluster XREF Gene #Evidence    //Igor: create clusters of Genes from microarray exps
                          SAGE_tag ?SAGE_tag XREF Gene #SAGE_mapping_info 
                          YH_bait   ?YH XREF Bait_overlapping_gene ?Text// for yeast two hybrid data
                          YH_target ?YH XREF Target_overlapping_gene ?Text
                          3d_data ?3d_data XREF Gene // for NESGC structure information
                          Interaction ?Interaction
                          Anatomy_function ?Anatomy_function XREF Gene
                          Product_binds_matrix ?Position_Matrix XREF Bound_by_gene_product #Evidence
        Map_info  Map UNIQUE ?Map XREF Gene #Map_position
                  Well_ordered          // "on the line"
                  Hide_under ?Gene XREF Representative_for
                  Representative_for ?Gene XREF Hide_under
                  Positive Inside_rearr   ?Rearrangement XREF Gene_inside #Evidence
                           Positive_clone ?Clone XREF Positive_gene #Evidence
                  Negative Outside_rearr  ?Rearrangement XREF Gene_outside #Evidence
                           Negative_clone ?Clone XREF Negative_gene #Evidence
                  Mapping_data  2_point ?2_point_data
                                Multi_point ?Multi_pt_data
                                Pos_neg_data ?Pos_neg_data
                  Interpolated_map_position UNIQUE ?Map UNIQUE Float // for loci with CDSs but no real Map position
                  Landmark_gene // for those genes that will appear in genetic map of Genome Browser
                  Pseudo_map_position // should be added to flag those genes which have Map position tags that
                                      // were 'promoted' from Interpolated_map_position tags
        Reference ?Paper XREF Gene #Evidence
        Remark ?Text #Evidence
        Method UNIQUE ?Method

Proposed Changes

Unused tags

Suppressed

Detailed_description

Rescued_by_transgene

3d_data

Product_binds_matrix - Has probable uses for the future