Difference between revisions of "WormBase Model:Paper"
From WormBaseWiki
Jump to navigationJump to search (Created page with '__TOC__ WormBase Models == Curator Comments/Description == == Model == <pre> </pre> == Proposed Changes ==') |
|||
Line 11: | Line 11: | ||
== 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
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