New Paper Model - Model and Changes to Pipeline

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Back to Paper Pipeline

After the model are links to specifics about the changes.

Latest version of the model (didn't want to remove the last version, below this one, quite yet).

Tags in bold are changes.

       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



Here is the old model. Tags in BOLD were tags that would require changes.


       Name    CGC_name ?Paper_name XREF CGC_name_for
               PMID     ?Paper_name XREF PMID_for
               Medline_name ?Paper_name XREF Medline_name_for
               WM_abstract ?Paper_name XREF WM_abstract_name_for
               WBG_abstract    ?Paper_name XREF WBG_abstract_name_for
               Other_name ?Paper_name XREF Other_name_for // e.g. agriola etc ...
       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 ?Journal XREF Paper
                       Publisher UNIQUE Text
                       Editor ?Text            //used for books put in as whole objects
                       Page  UNIQUE  Text UNIQUE Text
                       Volume UNIQUE Text Text
                       Year UNIQUE Datetype   //changed from Int for Tristan to help WormBook links
                       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
       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



TO CHECK and CHANGE, if needed

  1. We need to check that Acquires Merge and Merge are in the correct order in the model -- I might have switched this.
  • This is okay.
  1. Erratum_in and Erratum_for
  2. In_book -- Fixed 2010 01 27 -- J
  3. WM_abstract name
  4. Contained_in and Contains
  5. XML Status Tag
  6. Primary data Tag
  7. Journals