New Paper Model - Model and Changes to Pipeline
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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
- This is okay.
