WormBase Model:CDS

WormBase Models

Model

/////////////////////////////////////////////////////////////////////////////////////////////////
//
// ?CDS class - To store all coding genes
//
/////////////////////////////////////////////////////////////////////////////////////////////////


?CDS    Evidence #Evidence
        SMap S_parent UNIQUE Sequence   UNIQUE ?Sequence   XREF CDS_child
                             Transposon UNIQUE ?Transposon XREF CDS_child
        Structure Source_exons Int UNIQUE Int
        DB_info Database ?Database ?Database_field UNIQUE ?Accession_number XREF CDS
                Protein_id ?Sequence UNIQUE Text UNIQUE Int // DB_info tag added [011030 krb]
                DB_remark ?Text #Evidence
        Origin  From_laboratory UNIQUE ?Laboratory
                Species UNIQUE ?Species
                Genetic_code UNIQUE ?Genetic_code // needed for one gene with selenocysteine!
        Properties Coding CDS UNIQUE Int UNIQUE Int
                          CDS_predicted_by ?Method Float // score of method
                          Prediction_status UNIQUE Predicted            // all CDSs must be one of these three things
                                                   Partially_confirmed
                                                   Confirmed
                   Isoform #Evidence
                   Start_not_found Int
                   End_not_found
                   Merge Text  // ar2 270106 added by request for StLoius
                   Split Text  // ar2 270106 added by request for StLoius
        Gene_regulation Trans_regulator ?Gene_regulation XREF Trans_regulator_seq // Wen [030804 krb]
                        Trans_target    ?Gene_regulation XREF Trans_regulated_seq // Wen
                        Cis_target      ?Gene_regulation XREF Cis_regulated_seq   // Wen
        Visible Gene UNIQUE ?Gene XREF Corresponding_CDS // when live 
                Gene_history UNIQUE ?Gene XREF Corresponding_CDS_history // when dead
                Corresponding_transcript ?Transcript XREF Corresponding_CDS #Evidence  // links CDS' to new-style ?Transcript objects, 1-to-1 relationship
                Corresponding_protein UNIQUE ?Protein XREF Corresponding_CDS #Evidence 
                Corresponding_PCR_product ?PCR_product XREF Overlaps_CDS // added for PCR mappings [010419 dl]
                Corresponding_oligo_set ?Oligo_set XREF Overlaps_CDS
                Matching_cDNA ?Sequence XREF Matching_CDS #Evidence
                Expr_pattern ?Expr_pattern XREF CDS
                RNAi_result ?RNAi XREF Predicted_gene // Lincoln RNAi [001213 dl]
                GO_term ?GO_term XREF CDS ?GO_code #Evidence
                Variation ?Variation XREF Predicted_CDS // replaces Has_allele tag in ?Sequence
                Microarray_results ?Microarray_results XREF CDS      //added for Microarray_results
                Reference ?Paper XREF CDS // added [011030 krb]
                Provisional_description ?Text #Evidence
                Detailed_description ?Text #Evidence
                Concise_description ?Text #Evidence
                Brief_identification UNIQUE ?Text #Evidence
                Confidential_remark ?Text
                SAGE_tag ?SAGE_tag XREF Predicted_CDS #SAGE_mapping_info
                YH_bait   ?YH XREF Bait_overlapping_CDS ?Text// for yeast two hybrid data
                YH_target ?YH XREF Target_overlapping_CDS ?Text
                3d_data ?3d_data XREF CDS
                //Structure_data ?Structure_data XREF Corresponding_CDS #Evidence
                Remark ?Text #Evidence
        Associated_feature ?Feature XREF Associated_with_CDS #Evidence
        Method UNIQUE ?Method

Tags not used

Expr_pattern

Provisional_description

Detailed_description

Concise_description

Confidential_remark

SAGE_tag

3d_data

Merge and Split under Properties can be removed Wash U no longer use them

Proposed Changes

Remove unised tags?