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 quite yet): 

       Paper_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 identifier, 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 ?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
                       Publication_date ?Text   //used to capture available publication data from PubMed, could be YYYY-MM-DD or YYYY-MM     
                       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
  3. WM_abstract name
  4. Contained_in and Contains
  5. Type - mapping of current to future Type
  6. Type - mapping incoming Type
  7. XML Status Tag
  8. Primary data Tag
  9. Journals
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