Difference between revisions of "WormBase Model:CDS"

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(Created page with '__TOC__ WormBase Models == Curator Comments/Description == == Model == <pre> </pre> == Proposed Changes ==')
 
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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

WormBase Models

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

Tags not used

Proposed Changes