Difference between revisions of "WormBase Model:CDS"
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== Model == | == Model == | ||
<pre> | <pre> | ||
+ | ///////////////////////////////////////////////////////////////////////////////////////////////// | ||
+ | // | ||
+ | // ?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 | ||
</pre> | </pre> | ||
+ | |||
+ | == Tags not used == | ||
== Proposed Changes == | == Proposed Changes == |
Revision as of 15:30, 9 August 2010
Curator Comments/Description
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