Difference between revisions of "New Paper Model - Model and Changes to Pipeline"
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Back to [[Paper Pipeline]] | Back to [[Paper Pipeline]] | ||
− | Here is the model. Tags in '''BOLD''' | + | 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. | ||
− | |||
Revision as of 17:54, 19 January 2010
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
- This is okay.