From be12868b221af404d97bbbd1e64603ecd1135e32 Mon Sep 17 00:00:00 2001 From: Doug Manuel Date: Fri, 28 Aug 2026 14:33:42 -0400 Subject: [PATCH 1/2] Citation store: refresh Zotero metadata and URIs for six items In both field-codes.json files (protocol and manuscript), Manuel_HR_2020 carried the Health Canada item's Zotero URI, and Holford_AJPM_2014, Tam_AJPM_2023, Meza_J_2021 (and Rao_SM_1992 in the protocol store) had placeholder ids with no URI. Re-fetched all six from the Zotero library (Better BibTeX citekeys match); Tam_AJPM_2023 points at the Brazil paper (TZBN3JTZ), not the same-issue editorial that the citekey lookup returned. Holford_SM_2006, StatCan_CCHS_UserGuide_2022 and mitra2015 remain without URIs: they are not in the Zotero library. --- _docstyle/field-codes.json | 52 ++++++++++++------ docs/protocol/_docstyle/field-codes.json | 69 +++++++++++++++--------- docs/protocol/_docstyle/section-map.json | 59 ++++++++++++++------ 3 files changed, 121 insertions(+), 59 deletions(-) diff --git a/_docstyle/field-codes.json b/_docstyle/field-codes.json index 65e2941..e14766c 100644 --- a/_docstyle/field-codes.json +++ b/_docstyle/field-codes.json @@ -12,17 +12,13 @@ "title": "Smoking and mortality", "URL": "https://www.canada.ca/en/health-canada/services/health-concerns/tobacco/legislation/tobacco-product-labelling/smoking-mortality.html", "author": [ - { - "literal": "Health Canada" - } + {"literal": "Health Canada"} ], "issued": { "date-parts": [["2024"]] } }, - "uris": [ - "http://zotero.org/users/6858935/items/BIVEE78X" - ] + "uris": ["http://zotero.org/users/6858935/items/BIVEE78X"] }, "CSUCH_2023": { "itemData": { @@ -243,10 +239,13 @@ "id": 2357, "type": "article-journal", "citation-key": "Holford_AJPM_2014", - "container-title": "American Journal of Preventive Medicine", + "abstract": "BACKGROUND: Characterizing the smoking patterns for different birth cohorts is essential for evaluating the impact of tobacco control interventions and predicting smoking-related mortality, but the process of estimating birth cohort smoking histories has received limited attention. PURPOSE: Smoking history summaries were estimated beginning with the 1890 birth cohort in order to provide fundamental parameters that can be used in studies of cigarette smoking intervention strategies. METHODS: U.S. National Health Interview Surveys conducted from 1965 to 2009 were used to obtain cross-sectional information on current smoking behavior. Surveys that provided additional detail on history for smokers including age at initiation and cessation and smoking intensity were used to construct smoking histories for participants up to the date of survey. After incorporating survival differences by smoking status, age-period-cohort models with constrained natural splines were used to estimate the prevalence of current, former, and never smokers in cohorts beginning in 1890. This approach was then used to obtain yearly estimates of initiation, cessation, and smoking intensity for the age-specific distribution for each birth cohort. These rates were projected forward through 2050 based on recent trends. RESULTS: This summary of smoking history shows clear trends by gender, cohort, and age over time. If current patterns persist, a slow decline in smoking prevalence is projected from 2010 through 2040. CONCLUSIONS: A novel method of generating smoking histories has been applied to develop smoking histories that can be used in micro-simulation models, and has been incorporated in the National Cancer Institute's Smoking History Generator. These aggregate estimates developed by age, gender, and cohort will provide a complete source of smoking data over time.", + "container-title": "Am J Prev Med", "DOI": "10.1016/j.amepre.2013.10.022", + "ISSN": "1873-2607 (Electronic) 0749-3797 (Linking)", "issue": "2", "page": "e31-7", + "PMCID": "PMC3951759", "title": "Patterns of birth cohort-specific smoking histories, 1965-2009", "volume": "46", "author": [ @@ -261,9 +260,10 @@ {"family": "Feuer", "given": "E. J."} ], "issued": { - "date-parts": [["2014"]] + "date-parts": [["2014", 2]] } - } + }, + "uris": ["http://zotero.org/users/6858935/items/ATK94TD6"] }, "Manuel_HR_2020": { "itemData": { @@ -275,6 +275,7 @@ "ISSN": "0840-6529", "issue": "11", "page": "16-31", + "PMCID": "PMC3951759", "title": "Smoking patterns based on birth-cohort-specific histories from 1965 to 2013, with projections to 2041", "URL": "https://www150.statcan.gc.ca/n1/pub/82-003-x/2020011/article/00002-eng.htm", "volume": "31", @@ -290,9 +291,7 @@ "date-parts": [["2020"]] } }, - "uris": [ - "http://zotero.org/users/6858935/items/BIVEE78X" - ] + "uris": ["http://zotero.org/users/6858935/items/K5TKC5RV"] }, "Tam_AJPM_2023": { "itemData": { @@ -301,9 +300,14 @@ "citation-key": "Tam_AJPM_2023", "container-title": "American Journal of Preventive Medicine", "DOI": "10.1016/j.amepre.2022.12.002", + "ISSN": "07493797", "issue": "4", + "journalAbbreviation": "Am. J. Prev. Med.", + "language": "en", "page": "S63-S71", - "title": "Patterns of birth cohort-specific smoking histories in Brazil", + "source": "DOI.org (Crossref)", + "title": "Patterns of birth cohort‒specific smoking histories in Brazil", + "URL": "https://linkinghub.elsevier.com/retrieve/pii/S0749379722005530", "volume": "64", "author": [ {"family": "Tam", "given": "Jamie"}, @@ -318,10 +322,14 @@ {"family": "Sánchez-Romero", "given": "Luz M."}, {"family": "Meza", "given": "Rafael"} ], + "accessed": { + "date-parts": [["2025", 6, 20]] + }, "issued": { - "date-parts": [["2023"]] + "date-parts": [["2023", 4]] } - } + }, + "uris": ["http://zotero.org/users/6858935/items/TZBN3JTZ"] }, "gagne2017": { "itemData": { @@ -468,9 +476,15 @@ "citation-key": "Meza_J_2021", "container-title": "JAMA", "DOI": "10.1001/jama.2021.1077", + "ISSN": "0098-7484", "issue": "10", + "journalAbbreviation": "JAMA", + "language": "en", "page": "988", + "source": "DOI.org (Crossref)", "title": "Evaluation of the benefits and harms of lung cancer screening with low-dose computed tomography: modeling study for the US preventive services task force", + "title-short": "Evaluation of the benefits and harms of lung cancer screening with low-dose computed tomography", + "URL": "https://jamanetwork.com/journals/jama/fullarticle/2777243", "volume": "325", "author": [ {"family": "Meza", "given": "Rafael"}, @@ -487,10 +501,14 @@ {"family": "De Koning", "given": "Harry J."}, {"family": "Kong", "given": "Chung Yin"} ], + "accessed": { + "date-parts": [["2026", 2, 20]] + }, "issued": { - "date-parts": [["2021"]] + "date-parts": [["2021", 3, 9]] } - } + }, + "uris": ["http://zotero.org/users/6858935/items/NUDAXFIV"] } } } diff --git a/docs/protocol/_docstyle/field-codes.json b/docs/protocol/_docstyle/field-codes.json index 6c83ca9..9f3c039 100644 --- a/docs/protocol/_docstyle/field-codes.json +++ b/docs/protocol/_docstyle/field-codes.json @@ -12,17 +12,13 @@ "title": "Smoking and mortality", "URL": "https://www.canada.ca/en/health-canada/services/health-concerns/tobacco/legislation/tobacco-product-labelling/smoking-mortality.html", "author": [ - { - "literal": "Health Canada" - } + {"literal": "Health Canada"} ], "issued": { "date-parts": [["2024"]] } }, - "uris": [ - "http://zotero.org/users/6858935/items/BIVEE78X" - ] + "uris": ["http://zotero.org/users/6858935/items/BIVEE78X"] }, "CSUCH_2023": { "itemData": { @@ -243,10 +239,13 @@ "id": 2357, "type": "article-journal", "citation-key": "Holford_AJPM_2014", - "container-title": "American Journal of Preventive Medicine", + "abstract": "BACKGROUND: Characterizing the smoking patterns for different birth cohorts is essential for evaluating the impact of tobacco control interventions and predicting smoking-related mortality, but the process of estimating birth cohort smoking histories has received limited attention. PURPOSE: Smoking history summaries were estimated beginning with the 1890 birth cohort in order to provide fundamental parameters that can be used in studies of cigarette smoking intervention strategies. METHODS: U.S. National Health Interview Surveys conducted from 1965 to 2009 were used to obtain cross-sectional information on current smoking behavior. Surveys that provided additional detail on history for smokers including age at initiation and cessation and smoking intensity were used to construct smoking histories for participants up to the date of survey. After incorporating survival differences by smoking status, age-period-cohort models with constrained natural splines were used to estimate the prevalence of current, former, and never smokers in cohorts beginning in 1890. This approach was then used to obtain yearly estimates of initiation, cessation, and smoking intensity for the age-specific distribution for each birth cohort. These rates were projected forward through 2050 based on recent trends. RESULTS: This summary of smoking history shows clear trends by gender, cohort, and age over time. If current patterns persist, a slow decline in smoking prevalence is projected from 2010 through 2040. CONCLUSIONS: A novel method of generating smoking histories has been applied to develop smoking histories that can be used in micro-simulation models, and has been incorporated in the National Cancer Institute's Smoking History Generator. These aggregate estimates developed by age, gender, and cohort will provide a complete source of smoking data over time.", + "container-title": "Am J Prev Med", "DOI": "10.1016/j.amepre.2013.10.022", + "ISSN": "1873-2607 (Electronic) 0749-3797 (Linking)", "issue": "2", "page": "e31-7", + "PMCID": "PMC3951759", "title": "Patterns of birth cohort-specific smoking histories, 1965-2009", "volume": "46", "author": [ @@ -261,9 +260,10 @@ {"family": "Feuer", "given": "E. J."} ], "issued": { - "date-parts": [["2014"]] + "date-parts": [["2014", 2]] } - } + }, + "uris": ["http://zotero.org/users/6858935/items/ATK94TD6"] }, "Manuel_HR_2020": { "itemData": { @@ -275,6 +275,7 @@ "ISSN": "0840-6529", "issue": "11", "page": "16-31", + "PMCID": "PMC3951759", "title": "Smoking patterns based on birth-cohort-specific histories from 1965 to 2013, with projections to 2041", "URL": "https://www150.statcan.gc.ca/n1/pub/82-003-x/2020011/article/00002-eng.htm", "volume": "31", @@ -290,9 +291,7 @@ "date-parts": [["2020"]] } }, - "uris": [ - "http://zotero.org/users/6858935/items/BIVEE78X" - ] + "uris": ["http://zotero.org/users/6858935/items/K5TKC5RV"] }, "Tam_AJPM_2023": { "itemData": { @@ -301,9 +300,14 @@ "citation-key": "Tam_AJPM_2023", "container-title": "American Journal of Preventive Medicine", "DOI": "10.1016/j.amepre.2022.12.002", + "ISSN": "07493797", "issue": "4", + "journalAbbreviation": "Am. J. Prev. Med.", + "language": "en", "page": "S63-S71", - "title": "Patterns of birth cohort-specific smoking histories in Brazil", + "source": "DOI.org (Crossref)", + "title": "Patterns of birth cohort‒specific smoking histories in Brazil", + "URL": "https://linkinghub.elsevier.com/retrieve/pii/S0749379722005530", "volume": "64", "author": [ {"family": "Tam", "given": "Jamie"}, @@ -318,10 +322,14 @@ {"family": "Sánchez-Romero", "given": "Luz M."}, {"family": "Meza", "given": "Rafael"} ], + "accessed": { + "date-parts": [["2025", 6, 20]] + }, "issued": { - "date-parts": [["2023"]] + "date-parts": [["2023", 4]] } - } + }, + "uris": ["http://zotero.org/users/6858935/items/TZBN3JTZ"] }, "gagne2017": { "itemData": { @@ -468,9 +476,15 @@ "citation-key": "Meza_J_2021", "container-title": "JAMA", "DOI": "10.1001/jama.2021.1077", + "ISSN": "0098-7484", "issue": "10", + "journalAbbreviation": "JAMA", + "language": "en", "page": "988", + "source": "DOI.org (Crossref)", "title": "Evaluation of the benefits and harms of lung cancer screening with low-dose computed tomography: modeling study for the US preventive services task force", + "title-short": "Evaluation of the benefits and harms of lung cancer screening with low-dose computed tomography", + "URL": "https://jamanetwork.com/journals/jama/fullarticle/2777243", "volume": "325", "author": [ {"family": "Meza", "given": "Rafael"}, @@ -487,10 +501,14 @@ {"family": "De Koning", "given": "Harry J."}, {"family": "Kong", "given": "Chung Yin"} ], + "accessed": { + "date-parts": [["2026", 2, 20]] + }, "issued": { - "date-parts": [["2021"]] + "date-parts": [["2021", 3, 9]] } - } + }, + "uris": ["http://zotero.org/users/6858935/items/NUDAXFIV"] }, "Holford_SM_2006": { "itemData": { @@ -516,20 +534,21 @@ "id": 99908, "type": "article-journal", "citation-key": "Rao_SM_1992", + "container-title": "Survey Methodology", + "issue": "2", + "page": "209-217", + "title": "Some recent work on resampling methods for complex surveys", + "volume": "18", "author": [ {"family": "Rao", "given": "J. N. K."}, {"family": "Wu", "given": "C. F. J."}, {"family": "Yue", "given": "K."} ], - "container-title": "Survey Methodology", - "issue": "2", "issued": { - "date-parts": [[1992]] - }, - "page": "209-217", - "title": "Some recent work on resampling methods for complex surveys", - "volume": "18" - } + "date-parts": [["1992"]] + } + }, + "uris": ["http://zotero.org/users/6858935/items/T3J86DHU"] }, "StatCan_CCHS_UserGuide_2022": { "itemData": { diff --git a/docs/protocol/_docstyle/section-map.json b/docs/protocol/_docstyle/section-map.json index bd5f04f..4bd14ae 100644 --- a/docs/protocol/_docstyle/section-map.json +++ b/docs/protocol/_docstyle/section-map.json @@ -12,46 +12,46 @@ { "index": 1, "section_class": "section-body", - "para_position": 201, + "para_position": 202, "is_closing": true, "line_numbers": "continuous", "field_code_payload": { "type": "section", "version": 2, - "line-numbers": "continuous", - "class": "section-body" + "class": "section-body", + "line-numbers": "continuous" } }, { "index": 2, "section_class": "section-body", - "para_position": 201, + "para_position": 202, "is_closing": false, "line_numbers": "none", "field_code_payload": { "type": "section", "version": 2, - "line-numbers": "continuous", - "class": "section-body-end" + "class": "section-body-end", + "line-numbers": "continuous" } }, { "index": 3, "section_class": "section-body", - "para_position": 245, + "para_position": 246, "is_closing": true, "line_numbers": "none", "field_code_payload": { "type": "section", "version": 2, - "page-break": true, - "class": "section-body" + "class": "section-body", + "page-break": true } }, { "index": 4, "section_class": "section-body", - "para_position": 245, + "para_position": 246, "is_closing": false, "line_numbers": "none", "field_code_payload": { @@ -63,20 +63,20 @@ { "index": 5, "section_class": "section-body", - "para_position": 251, + "para_position": 252, "is_closing": true, "line_numbers": "none", "field_code_payload": { "type": "section", "version": 2, - "page-break": true, - "class": "section-body" + "class": "section-body", + "page-break": true } }, { "index": 6, "section_class": "section-body", - "para_position": 251, + "para_position": 252, "is_closing": false, "line_numbers": "none", "field_code_payload": { @@ -88,18 +88,43 @@ { "index": 7, "section_class": "section-body", - "para_position": 256, + "para_position": 257, "is_closing": true, "line_numbers": "none", "field_code_payload": { "type": "section", "version": 2, - "page-break": true, - "class": "section-body" + "class": "section-body", + "page-break": true } }, { "index": 8, + "section_class": "section-body", + "para_position": 257, + "is_closing": false, + "line_numbers": "none", + "field_code_payload": { + "type": "section", + "version": 2, + "class": "section-body-end" + } + }, + { + "index": 9, + "section_class": "section-body", + "para_position": 270, + "is_closing": true, + "line_numbers": "none", + "field_code_payload": { + "type": "section", + "version": 2, + "class": "section-body", + "page-break": true + } + }, + { + "index": 10, "section_class": "final-cascade", "para_position": null, "is_closing": true, From d2ea087a13b888b5888b5e57a224a49621591371 Mon Sep 17 00:00:00 2001 From: Doug Manuel Date: Fri, 28 Aug 2026 15:58:06 -0400 Subject: [PATCH 2/2] Citation store: Zotero URIs for Holford 2006, Mitra 2015 and the CCHS user guide The three items were added to the Zotero library (_inbox collection) with their citekeys pinned via Better BibTeX, so every entry in both field-codes.json files now carries a Zotero URI. --- _docstyle/field-codes.json | 3 ++- docs/protocol/_docstyle/field-codes.json | 9 ++++++--- docs/protocol/_docstyle/section-map.json | 24 ++++++++++++------------ 3 files changed, 20 insertions(+), 16 deletions(-) diff --git a/_docstyle/field-codes.json b/_docstyle/field-codes.json index e14766c..7d71e00 100644 --- a/_docstyle/field-codes.json +++ b/_docstyle/field-codes.json @@ -64,7 +64,8 @@ "issued": { "date-parts": [["2015", "6"]] } - } + }, + "uris": ["http://zotero.org/users/6858935/items/VVX5CUHD"] }, "hennessy2015": { "itemData": { diff --git a/docs/protocol/_docstyle/field-codes.json b/docs/protocol/_docstyle/field-codes.json index 9f3c039..c26d936 100644 --- a/docs/protocol/_docstyle/field-codes.json +++ b/docs/protocol/_docstyle/field-codes.json @@ -64,7 +64,8 @@ "issued": { "date-parts": [["2015", "6"]] } - } + }, + "uris": ["http://zotero.org/users/6858935/items/VVX5CUHD"] }, "hennessy2015": { "itemData": { @@ -527,7 +528,8 @@ "page": "977-993", "title": "Approaches to fitting age-period-cohort models with unequal intervals", "volume": "25" - } + }, + "uris": ["http://zotero.org/users/6858935/items/C3C6KJD2"] }, "Rao_SM_1992": { "itemData": { @@ -564,7 +566,8 @@ "publisher": "Statistics Canada", "publisher-place": "Ottawa", "title": "Canadian community health survey (CCHS) – annual component: User guide, 2022 microdata file" - } + }, + "uris": ["http://zotero.org/users/6858935/items/E49I6Q3W"] } } } diff --git a/docs/protocol/_docstyle/section-map.json b/docs/protocol/_docstyle/section-map.json index 4bd14ae..e64d6bd 100644 --- a/docs/protocol/_docstyle/section-map.json +++ b/docs/protocol/_docstyle/section-map.json @@ -18,8 +18,8 @@ "field_code_payload": { "type": "section", "version": 2, - "class": "section-body", - "line-numbers": "continuous" + "line-numbers": "continuous", + "class": "section-body" } }, { @@ -31,8 +31,8 @@ "field_code_payload": { "type": "section", "version": 2, - "class": "section-body-end", - "line-numbers": "continuous" + "line-numbers": "continuous", + "class": "section-body-end" } }, { @@ -44,8 +44,8 @@ "field_code_payload": { "type": "section", "version": 2, - "class": "section-body", - "page-break": true + "page-break": true, + "class": "section-body" } }, { @@ -69,8 +69,8 @@ "field_code_payload": { "type": "section", "version": 2, - "class": "section-body", - "page-break": true + "page-break": true, + "class": "section-body" } }, { @@ -94,8 +94,8 @@ "field_code_payload": { "type": "section", "version": 2, - "class": "section-body", - "page-break": true + "page-break": true, + "class": "section-body" } }, { @@ -119,8 +119,8 @@ "field_code_payload": { "type": "section", "version": 2, - "class": "section-body", - "page-break": true + "page-break": true, + "class": "section-body" } }, {