WormBase Model:Paper

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WormBase Models

Curator Comments/Description

Model

// ?Paper class - krb 040223
// ?Paper class - krb 040223
// ID-based system (WBPaperXXXXXXXX) to allow paper tracking and an associated ?Paper_name class
//
////////////////////////////////////////////////////////////////////////////////////////////////////////

?Paper Original_timestamp Datetype // temporary tag in transition period [krb 040223]
       Name ?Text     //used for storing legacy names, like cgc5654 or wm95p426
       DB_info Database ?Database ?Database_field ?Accession_number     //used for storing PubMed or other database identifiers, for PubMed, Database_field would be PMID 
       History Merged_into UNIQUE ?Paper XREF Acquires_merge
               Acquires_merge ?Paper XREF Merged_into
       Status  Valid
               Invalid
       Erratum_in      ?Paper XREF Erratum_for
       Erratum_for     ?Paper XREF Erratum_in
       Reference       Title UNIQUE ?Text
                       Journal UNIQUE ?Text     //we are cleaning up Journal names and considering retiring the class
                       Publisher UNIQUE Text
                       Editor ?Text            //used for books put in as objects
                       Page  UNIQUE  Text 
                       Volume UNIQUE Text
                       Publication_date UNIQUE ?Text         //YYYY-MM-DD or YYYY-MM, replaces DateType which led to erroneous pub dates
                       Contained_in ?Paper XREF Contains       // old form
                       Contains ?Paper XREF Contained_in
       Author ?Author XREF Paper #Affiliation
       Person ?Person XREF Paper #Evidence
       Describes_analysis ?Analysis XREF Reference
       Not_person ?Person XREF Not_Paper #Evidence
       Affiliation Text        // Authors' affiliation if available
       Brief_citation UNIQUE Text
       Abstract ?LongText
       URL Text   //will be used for Worm Breeder's Gazette articles and other citations available online but not through PubMed
       Type    Journal_article        #Evidence
               Review        #Evidence
               Comment        #Evidence
               News        #Evidence
               Letter        #Evidence
               Editorial        #Evidence
               Congresses        #Evidence
               Historical_article        #Evidence
               Biography        #Evidence
               Interview        #Evidence
               Lectures        #Evidence
               Interactive_tutorial        #Evidence
               Retracted_publication        #Evidence
               Technical_report        #Evidence
               Directory        #Evidence
               Monograph        #Evidence
               Published_erratum        #Evidence
               Meeting_abstract        #Evidence
               Gazette_article        #Evidence
               Book_chapter        #Evidence
               Book        #Evidence
               Email        #Evidence
               WormBook        #Evidence
               Other        #Evidence
       Refers_to Gene ?Gene XREF Reference #Evidence
                 Allele ?Variation XREF Reference #Evidence
                 Rearrangement ?Rearrangement XREF Reference #Evidence
                 Sequence ?Sequence XREF Reference #Evidence
                 CDS ?CDS XREF Reference #Evidence
                 Transcript ?Transcript XREF Reference #Evidence
                 Strain ?Strain XREF Reference #Evidence
                 Clone ?Clone XREF Reference #Evidence
                 Expr_pattern ?Expr_pattern XREF Reference #Evidence
                 Expr_profile ?Expr_profile XREF Reference #Evidence
                 Cell ?Cell XREF Reference #Evidence
                 Cell_group ?Cell_group XREF Reference #Evidence
                 Life_stage ?Life_stage XREF Reference #Evidence
                 RNAi ?RNAi XREF Reference #Evidence
                 Transgene ?Transgene XREF Reference #Evidence
                 Operon ?Operon XREF Reference #Evidence
                 Expression_cluster ?Expression_cluster XREF Reference #Evidence
                 Feature ?Feature XREF Defined_by_paper                 // added [030424 dl]
                 Gene_regulation ?Gene_regulation XREF Reference // added [030804 krb]
                 Microarray_experiment ?Microarray_experiment XREF Reference //added for Microarray_experiment model
                 Anatomy_term ?Anatomy_term XREF Reference #Evidence
                 Anatomy_function ?Anatomy_function XREF Reference
                 Antibody ?Antibody XREF Reference #Evidence // added [031120 krb]
                 SAGE_experiment ?SAGE_experiment XREF Reference
                 YH ?YH XREF Reference ?Text
                 Interaction ?Interaction XREF Paper
                 Mass_spec_experiment ?Mass_spec_experiment XREF Reference
       Curation_pipeline Phenotype2GO
       Keyword ?Keyword
       Remark  ?Text   #Evidence

Proposed Changes

Unused tags

Original_timestamp

Type Directory

Type Email

Refers_to Operon

Refers_to Anatomy_term