Difference between revisions of "WormBase Model:Paper"

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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>
 +
// ?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
  
 
</pre>
 
</pre>
  
 
== Proposed Changes ==
 
== Proposed Changes ==
 +
 +
==Unused tags==
 +
Original_timestamp
 +
 +
Type Directory
 +
 +
Type Email
 +
 +
Refers_to Operon
 +
 +
Refers_to Anatomy_term

Latest revision as of 16:07, 4 October 2010

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