scientific-writer 2.1.1__py3-none-any.whl → 2.2.2__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.


This version of scientific-writer might be problematic. Click here for more details.

Files changed (311) hide show
  1. scientific_writer/.claude/settings.local.json +30 -0
  2. scientific_writer/.claude/skills/citation-management/SKILL.md +1046 -0
  3. scientific_writer/.claude/skills/citation-management/assets/bibtex_template.bib +264 -0
  4. scientific_writer/.claude/skills/citation-management/assets/citation_checklist.md +386 -0
  5. scientific_writer/.claude/skills/citation-management/references/bibtex_formatting.md +908 -0
  6. scientific_writer/.claude/skills/citation-management/references/citation_validation.md +794 -0
  7. scientific_writer/.claude/skills/citation-management/references/google_scholar_search.md +725 -0
  8. scientific_writer/.claude/skills/citation-management/references/metadata_extraction.md +870 -0
  9. scientific_writer/.claude/skills/citation-management/references/pubmed_search.md +839 -0
  10. scientific_writer/.claude/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
  11. scientific_writer/.claude/skills/citation-management/scripts/extract_metadata.py +569 -0
  12. scientific_writer/.claude/skills/citation-management/scripts/format_bibtex.py +349 -0
  13. scientific_writer/.claude/skills/citation-management/scripts/search_google_scholar.py +282 -0
  14. scientific_writer/.claude/skills/citation-management/scripts/search_pubmed.py +398 -0
  15. scientific_writer/.claude/skills/citation-management/scripts/validate_citations.py +497 -0
  16. scientific_writer/.claude/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +641 -0
  17. scientific_writer/.claude/skills/clinical-reports/README.md +236 -0
  18. scientific_writer/.claude/skills/clinical-reports/SKILL.md +1088 -0
  19. scientific_writer/.claude/skills/clinical-reports/assets/case_report_template.md +352 -0
  20. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
  21. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
  22. scientific_writer/.claude/skills/clinical-reports/assets/consult_note_template.md +305 -0
  23. scientific_writer/.claude/skills/clinical-reports/assets/discharge_summary_template.md +453 -0
  24. scientific_writer/.claude/skills/clinical-reports/assets/hipaa_compliance_checklist.md +395 -0
  25. scientific_writer/.claude/skills/clinical-reports/assets/history_physical_template.md +305 -0
  26. scientific_writer/.claude/skills/clinical-reports/assets/lab_report_template.md +309 -0
  27. scientific_writer/.claude/skills/clinical-reports/assets/pathology_report_template.md +249 -0
  28. scientific_writer/.claude/skills/clinical-reports/assets/quality_checklist.md +338 -0
  29. scientific_writer/.claude/skills/clinical-reports/assets/radiology_report_template.md +318 -0
  30. scientific_writer/.claude/skills/clinical-reports/assets/soap_note_template.md +253 -0
  31. scientific_writer/.claude/skills/clinical-reports/references/case_report_guidelines.md +570 -0
  32. scientific_writer/.claude/skills/clinical-reports/references/clinical_trial_reporting.md +693 -0
  33. scientific_writer/.claude/skills/clinical-reports/references/data_presentation.md +530 -0
  34. scientific_writer/.claude/skills/clinical-reports/references/diagnostic_reports_standards.md +629 -0
  35. scientific_writer/.claude/skills/clinical-reports/references/medical_terminology.md +588 -0
  36. scientific_writer/.claude/skills/clinical-reports/references/patient_documentation.md +744 -0
  37. scientific_writer/.claude/skills/clinical-reports/references/peer_review_standards.md +585 -0
  38. scientific_writer/.claude/skills/clinical-reports/references/regulatory_compliance.md +577 -0
  39. scientific_writer/.claude/skills/clinical-reports/scripts/check_deidentification.py +346 -0
  40. scientific_writer/.claude/skills/clinical-reports/scripts/compliance_checker.py +78 -0
  41. scientific_writer/.claude/skills/clinical-reports/scripts/extract_clinical_data.py +102 -0
  42. scientific_writer/.claude/skills/clinical-reports/scripts/format_adverse_events.py +103 -0
  43. scientific_writer/.claude/skills/clinical-reports/scripts/generate_report_template.py +163 -0
  44. scientific_writer/.claude/skills/clinical-reports/scripts/terminology_validator.py +133 -0
  45. scientific_writer/.claude/skills/clinical-reports/scripts/validate_case_report.py +334 -0
  46. scientific_writer/.claude/skills/clinical-reports/scripts/validate_trial_report.py +89 -0
  47. scientific_writer/.claude/skills/document-skills/docx/LICENSE.txt +30 -0
  48. scientific_writer/.claude/skills/document-skills/docx/SKILL.md +197 -0
  49. scientific_writer/.claude/skills/document-skills/docx/docx-js.md +350 -0
  50. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  51. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  52. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  53. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  54. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  55. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  56. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  57. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  58. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  59. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  60. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  61. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  62. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  63. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  64. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  65. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  66. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  67. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  68. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  69. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  70. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  71. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  72. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  73. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  74. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  75. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  76. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  77. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  78. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  79. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  80. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  81. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +75 -0
  82. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  83. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  84. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  85. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  86. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  87. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  88. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  89. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/pack.py +159 -0
  90. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/unpack.py +29 -0
  91. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
  92. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
  93. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/base.py +951 -0
  94. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/docx.py +274 -0
  95. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +315 -0
  96. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +279 -0
  97. scientific_writer/.claude/skills/document-skills/docx/ooxml.md +610 -0
  98. scientific_writer/.claude/skills/document-skills/docx/scripts/__init__.py +1 -0
  99. scientific_writer/.claude/skills/document-skills/docx/scripts/document.py +1276 -0
  100. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/comments.xml +3 -0
  101. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtended.xml +3 -0
  102. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +3 -0
  103. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsIds.xml +3 -0
  104. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/people.xml +3 -0
  105. scientific_writer/.claude/skills/document-skills/docx/scripts/utilities.py +374 -0
  106. scientific_writer/.claude/skills/document-skills/pdf/LICENSE.txt +30 -0
  107. scientific_writer/.claude/skills/document-skills/pdf/SKILL.md +294 -0
  108. scientific_writer/.claude/skills/document-skills/pdf/forms.md +205 -0
  109. scientific_writer/.claude/skills/document-skills/pdf/reference.md +612 -0
  110. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes.py +70 -0
  111. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +226 -0
  112. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_fillable_fields.py +12 -0
  113. scientific_writer/.claude/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +35 -0
  114. scientific_writer/.claude/skills/document-skills/pdf/scripts/create_validation_image.py +41 -0
  115. scientific_writer/.claude/skills/document-skills/pdf/scripts/extract_form_field_info.py +152 -0
  116. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_fillable_fields.py +114 -0
  117. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +108 -0
  118. scientific_writer/.claude/skills/document-skills/pptx/LICENSE.txt +30 -0
  119. scientific_writer/.claude/skills/document-skills/pptx/SKILL.md +484 -0
  120. scientific_writer/.claude/skills/document-skills/pptx/html2pptx.md +625 -0
  121. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  122. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  123. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  124. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  125. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  126. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  127. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  128. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  129. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  130. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  131. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  132. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  133. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  134. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  135. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  136. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  137. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  138. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  139. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  140. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  141. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  142. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  143. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  144. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  145. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  146. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  147. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  148. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  149. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  150. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  151. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  152. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd +75 -0
  153. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  154. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  155. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  156. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  157. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  158. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  159. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  160. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/pack.py +159 -0
  161. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/unpack.py +29 -0
  162. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validate.py +69 -0
  163. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/__init__.py +15 -0
  164. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/base.py +951 -0
  165. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/docx.py +274 -0
  166. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/pptx.py +315 -0
  167. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/redlining.py +279 -0
  168. scientific_writer/.claude/skills/document-skills/pptx/ooxml.md +427 -0
  169. scientific_writer/.claude/skills/document-skills/pptx/scripts/html2pptx.js +979 -0
  170. scientific_writer/.claude/skills/document-skills/pptx/scripts/inventory.py +1020 -0
  171. scientific_writer/.claude/skills/document-skills/pptx/scripts/rearrange.py +231 -0
  172. scientific_writer/.claude/skills/document-skills/pptx/scripts/replace.py +385 -0
  173. scientific_writer/.claude/skills/document-skills/pptx/scripts/thumbnail.py +450 -0
  174. scientific_writer/.claude/skills/document-skills/xlsx/LICENSE.txt +30 -0
  175. scientific_writer/.claude/skills/document-skills/xlsx/SKILL.md +289 -0
  176. scientific_writer/.claude/skills/document-skills/xlsx/recalc.py +178 -0
  177. scientific_writer/.claude/skills/hypothesis-generation/SKILL.md +155 -0
  178. scientific_writer/.claude/skills/hypothesis-generation/assets/hypothesis_output_template.md +302 -0
  179. scientific_writer/.claude/skills/hypothesis-generation/references/experimental_design_patterns.md +327 -0
  180. scientific_writer/.claude/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +196 -0
  181. scientific_writer/.claude/skills/hypothesis-generation/references/literature_search_strategies.md +505 -0
  182. scientific_writer/.claude/skills/latex-posters/README.md +417 -0
  183. scientific_writer/.claude/skills/latex-posters/SKILL.md +919 -0
  184. scientific_writer/.claude/skills/latex-posters/assets/baposter_template.tex +257 -0
  185. scientific_writer/.claude/skills/latex-posters/assets/beamerposter_template.tex +244 -0
  186. scientific_writer/.claude/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
  187. scientific_writer/.claude/skills/latex-posters/assets/tikzposter_template.tex +251 -0
  188. scientific_writer/.claude/skills/latex-posters/references/latex_poster_packages.md +745 -0
  189. scientific_writer/.claude/skills/latex-posters/references/poster_content_guide.md +748 -0
  190. scientific_writer/.claude/skills/latex-posters/references/poster_design_principles.md +806 -0
  191. scientific_writer/.claude/skills/latex-posters/references/poster_layout_design.md +900 -0
  192. scientific_writer/.claude/skills/latex-posters/scripts/review_poster.sh +214 -0
  193. scientific_writer/.claude/skills/literature-review/SKILL.md +546 -0
  194. scientific_writer/.claude/skills/literature-review/assets/review_template.md +412 -0
  195. scientific_writer/.claude/skills/literature-review/references/citation_styles.md +166 -0
  196. scientific_writer/.claude/skills/literature-review/references/database_strategies.md +381 -0
  197. scientific_writer/.claude/skills/literature-review/scripts/generate_pdf.py +176 -0
  198. scientific_writer/.claude/skills/literature-review/scripts/search_databases.py +303 -0
  199. scientific_writer/.claude/skills/literature-review/scripts/verify_citations.py +222 -0
  200. scientific_writer/.claude/skills/markitdown/INSTALLATION_GUIDE.md +318 -0
  201. scientific_writer/.claude/skills/markitdown/LICENSE.txt +22 -0
  202. scientific_writer/.claude/skills/markitdown/OPENROUTER_INTEGRATION.md +359 -0
  203. scientific_writer/.claude/skills/markitdown/QUICK_REFERENCE.md +309 -0
  204. scientific_writer/.claude/skills/markitdown/README.md +184 -0
  205. scientific_writer/.claude/skills/markitdown/SKILL.md +450 -0
  206. scientific_writer/.claude/skills/markitdown/SKILL_SUMMARY.md +307 -0
  207. scientific_writer/.claude/skills/markitdown/assets/example_usage.md +463 -0
  208. scientific_writer/.claude/skills/markitdown/references/api_reference.md +399 -0
  209. scientific_writer/.claude/skills/markitdown/references/file_formats.md +542 -0
  210. scientific_writer/.claude/skills/markitdown/scripts/batch_convert.py +228 -0
  211. scientific_writer/.claude/skills/markitdown/scripts/convert_literature.py +283 -0
  212. scientific_writer/.claude/skills/markitdown/scripts/convert_with_ai.py +243 -0
  213. scientific_writer/.claude/skills/paper-2-web/SKILL.md +455 -0
  214. scientific_writer/.claude/skills/paper-2-web/references/installation.md +141 -0
  215. scientific_writer/.claude/skills/paper-2-web/references/paper2poster.md +346 -0
  216. scientific_writer/.claude/skills/paper-2-web/references/paper2video.md +305 -0
  217. scientific_writer/.claude/skills/paper-2-web/references/paper2web.md +187 -0
  218. scientific_writer/.claude/skills/paper-2-web/references/usage_examples.md +436 -0
  219. scientific_writer/.claude/skills/peer-review/SKILL.md +375 -0
  220. scientific_writer/.claude/skills/peer-review/references/common_issues.md +552 -0
  221. scientific_writer/.claude/skills/peer-review/references/reporting_standards.md +290 -0
  222. scientific_writer/.claude/skills/research-grants/README.md +285 -0
  223. scientific_writer/.claude/skills/research-grants/SKILL.md +896 -0
  224. scientific_writer/.claude/skills/research-grants/assets/budget_justification_template.md +453 -0
  225. scientific_writer/.claude/skills/research-grants/assets/nih_specific_aims_template.md +166 -0
  226. scientific_writer/.claude/skills/research-grants/assets/nsf_project_summary_template.md +92 -0
  227. scientific_writer/.claude/skills/research-grants/references/broader_impacts.md +392 -0
  228. scientific_writer/.claude/skills/research-grants/references/darpa_guidelines.md +636 -0
  229. scientific_writer/.claude/skills/research-grants/references/doe_guidelines.md +586 -0
  230. scientific_writer/.claude/skills/research-grants/references/nih_guidelines.md +851 -0
  231. scientific_writer/.claude/skills/research-grants/references/nsf_guidelines.md +570 -0
  232. scientific_writer/.claude/skills/research-grants/references/specific_aims_guide.md +458 -0
  233. scientific_writer/.claude/skills/research-lookup/README.md +116 -0
  234. scientific_writer/.claude/skills/research-lookup/SKILL.md +443 -0
  235. scientific_writer/.claude/skills/research-lookup/examples.py +174 -0
  236. scientific_writer/.claude/skills/research-lookup/lookup.py +93 -0
  237. scientific_writer/.claude/skills/research-lookup/research_lookup.py +335 -0
  238. scientific_writer/.claude/skills/research-lookup/scripts/research_lookup.py +261 -0
  239. scientific_writer/.claude/skills/scholar-evaluation/SKILL.md +254 -0
  240. scientific_writer/.claude/skills/scholar-evaluation/references/evaluation_framework.md +663 -0
  241. scientific_writer/.claude/skills/scholar-evaluation/scripts/calculate_scores.py +378 -0
  242. scientific_writer/.claude/skills/scientific-critical-thinking/SKILL.md +530 -0
  243. scientific_writer/.claude/skills/scientific-critical-thinking/references/common_biases.md +364 -0
  244. scientific_writer/.claude/skills/scientific-critical-thinking/references/evidence_hierarchy.md +484 -0
  245. scientific_writer/.claude/skills/scientific-critical-thinking/references/experimental_design.md +496 -0
  246. scientific_writer/.claude/skills/scientific-critical-thinking/references/logical_fallacies.md +478 -0
  247. scientific_writer/.claude/skills/scientific-critical-thinking/references/scientific_method.md +169 -0
  248. scientific_writer/.claude/skills/scientific-critical-thinking/references/statistical_pitfalls.md +506 -0
  249. scientific_writer/.claude/skills/scientific-schematics/SKILL.md +2035 -0
  250. scientific_writer/.claude/skills/scientific-schematics/assets/block_diagram_template.tex +199 -0
  251. scientific_writer/.claude/skills/scientific-schematics/assets/circuit_template.tex +159 -0
  252. scientific_writer/.claude/skills/scientific-schematics/assets/flowchart_template.tex +161 -0
  253. scientific_writer/.claude/skills/scientific-schematics/assets/pathway_template.tex +162 -0
  254. scientific_writer/.claude/skills/scientific-schematics/assets/tikz_styles.tex +422 -0
  255. scientific_writer/.claude/skills/scientific-schematics/references/best_practices.md +562 -0
  256. scientific_writer/.claude/skills/scientific-schematics/references/diagram_types.md +637 -0
  257. scientific_writer/.claude/skills/scientific-schematics/references/python_libraries.md +791 -0
  258. scientific_writer/.claude/skills/scientific-schematics/references/tikz_guide.md +734 -0
  259. scientific_writer/.claude/skills/scientific-schematics/scripts/circuit_generator.py +307 -0
  260. scientific_writer/.claude/skills/scientific-schematics/scripts/compile_tikz.py +292 -0
  261. scientific_writer/.claude/skills/scientific-schematics/scripts/generate_flowchart.py +281 -0
  262. scientific_writer/.claude/skills/scientific-schematics/scripts/pathway_diagram.py +406 -0
  263. scientific_writer/.claude/skills/scientific-writing/SKILL.md +443 -0
  264. scientific_writer/.claude/skills/scientific-writing/references/citation_styles.md +720 -0
  265. scientific_writer/.claude/skills/scientific-writing/references/figures_tables.md +806 -0
  266. scientific_writer/.claude/skills/scientific-writing/references/imrad_structure.md +658 -0
  267. scientific_writer/.claude/skills/scientific-writing/references/reporting_guidelines.md +748 -0
  268. scientific_writer/.claude/skills/scientific-writing/references/writing_principles.md +824 -0
  269. scientific_writer/.claude/skills/treatment-plans/README.md +483 -0
  270. scientific_writer/.claude/skills/treatment-plans/SKILL.md +817 -0
  271. scientific_writer/.claude/skills/treatment-plans/assets/chronic_disease_management_plan.tex +636 -0
  272. scientific_writer/.claude/skills/treatment-plans/assets/general_medical_treatment_plan.tex +616 -0
  273. scientific_writer/.claude/skills/treatment-plans/assets/mental_health_treatment_plan.tex +745 -0
  274. scientific_writer/.claude/skills/treatment-plans/assets/pain_management_plan.tex +770 -0
  275. scientific_writer/.claude/skills/treatment-plans/assets/perioperative_care_plan.tex +724 -0
  276. scientific_writer/.claude/skills/treatment-plans/assets/quality_checklist.md +471 -0
  277. scientific_writer/.claude/skills/treatment-plans/assets/rehabilitation_treatment_plan.tex +727 -0
  278. scientific_writer/.claude/skills/treatment-plans/references/goal_setting_frameworks.md +411 -0
  279. scientific_writer/.claude/skills/treatment-plans/references/intervention_guidelines.md +507 -0
  280. scientific_writer/.claude/skills/treatment-plans/references/regulatory_compliance.md +476 -0
  281. scientific_writer/.claude/skills/treatment-plans/references/specialty_specific_guidelines.md +607 -0
  282. scientific_writer/.claude/skills/treatment-plans/references/treatment_plan_standards.md +456 -0
  283. scientific_writer/.claude/skills/treatment-plans/scripts/check_completeness.py +318 -0
  284. scientific_writer/.claude/skills/treatment-plans/scripts/generate_template.py +244 -0
  285. scientific_writer/.claude/skills/treatment-plans/scripts/timeline_generator.py +369 -0
  286. scientific_writer/.claude/skills/treatment-plans/scripts/validate_treatment_plan.py +367 -0
  287. scientific_writer/.claude/skills/venue-templates/SKILL.md +590 -0
  288. scientific_writer/.claude/skills/venue-templates/assets/grants/nih_specific_aims.tex +235 -0
  289. scientific_writer/.claude/skills/venue-templates/assets/grants/nsf_proposal_template.tex +375 -0
  290. scientific_writer/.claude/skills/venue-templates/assets/journals/nature_article.tex +171 -0
  291. scientific_writer/.claude/skills/venue-templates/assets/journals/neurips_article.tex +283 -0
  292. scientific_writer/.claude/skills/venue-templates/assets/journals/plos_one.tex +317 -0
  293. scientific_writer/.claude/skills/venue-templates/assets/posters/beamerposter_academic.tex +311 -0
  294. scientific_writer/.claude/skills/venue-templates/references/conferences_formatting.md +564 -0
  295. scientific_writer/.claude/skills/venue-templates/references/grants_requirements.md +787 -0
  296. scientific_writer/.claude/skills/venue-templates/references/journals_formatting.md +486 -0
  297. scientific_writer/.claude/skills/venue-templates/references/posters_guidelines.md +628 -0
  298. scientific_writer/.claude/skills/venue-templates/scripts/customize_template.py +206 -0
  299. scientific_writer/.claude/skills/venue-templates/scripts/query_template.py +260 -0
  300. scientific_writer/.claude/skills/venue-templates/scripts/validate_format.py +255 -0
  301. scientific_writer/CLAUDE.md +748 -0
  302. scientific_writer/__init__.py +2 -2
  303. scientific_writer/api.py +14 -7
  304. scientific_writer/cli.py +12 -7
  305. scientific_writer/core.py +27 -5
  306. {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/METADATA +5 -1
  307. scientific_writer-2.2.2.dist-info/RECORD +312 -0
  308. scientific_writer-2.1.1.dist-info/RECORD +0 -11
  309. {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/WHEEL +0 -0
  310. {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/entry_points.txt +0 -0
  311. {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/licenses/LICENSE +0 -0
@@ -0,0 +1,577 @@
1
+ # Regulatory Compliance for Clinical Reports
2
+
3
+ ## HIPAA (Health Insurance Portability and Accountability Act)
4
+
5
+ ### Overview
6
+
7
+ HIPAA Privacy Rule protects individually identifiable health information (Protected Health Information, PHI). All clinical reports must comply with HIPAA requirements for privacy and security.
8
+
9
+ ### Protected Health Information (PHI)
10
+
11
+ **Definition:** Individually identifiable health information held or transmitted by covered entities or business associates in any form or medium.
12
+
13
+ **Covered Entities:**
14
+ - Healthcare providers
15
+ - Health plans
16
+ - Healthcare clearinghouses
17
+
18
+ **Business Associates:**
19
+ - Third parties providing services involving PHI
20
+ - Require Business Associate Agreement (BAA)
21
+
22
+ ### 18 HIPAA Identifiers
23
+
24
+ These identifiers must be removed for Safe Harbor de-identification:
25
+
26
+ 1. **Names**
27
+ 2. **Geographic subdivisions smaller than state** (except first 3 digits of ZIP if >20,000 people)
28
+ 3. **Dates** (except year) - birth, admission, discharge, death
29
+ 4. **Telephone numbers**
30
+ 5. **Fax numbers**
31
+ 6. **Email addresses**
32
+ 7. **Social Security numbers**
33
+ 8. **Medical record numbers**
34
+ 9. **Health plan beneficiary numbers**
35
+ 10. **Account numbers**
36
+ 11. **Certificate/license numbers**
37
+ 12. **Vehicle identifiers and serial numbers**
38
+ 13. **Device identifiers and serial numbers**
39
+ 14. **Web URLs**
40
+ 15. **IP addresses**
41
+ 16. **Biometric identifiers** (fingerprints, voiceprints)
42
+ 17. **Full-face photographs and comparable images**
43
+ 18. **Any other unique identifying characteristic or code**
44
+
45
+ ### De-identification Methods
46
+
47
+ #### Method 1: Safe Harbor
48
+
49
+ Remove all 18 identifiers AND have no actual knowledge that remaining information could be used to identify the individual.
50
+
51
+ **Implementation:**
52
+ - Remove/redact all 18 identifiers
53
+ - Ages over 89 must be aggregated to "90 or older"
54
+ - Dates can keep year only
55
+ - Geographic areas can include state only
56
+ - Documentation that no identifying information remains
57
+
58
+ #### Method 2: Expert Determination
59
+
60
+ Statistical/scientific analysis demonstrating that risk of re-identification is very small.
61
+
62
+ **Requirements:**
63
+ - Performed by qualified statistician or expert
64
+ - Documented analysis methods
65
+ - Conclusion that re-identification risk is very small
66
+ - Maintained documentation
67
+
68
+ ### HIPAA Minimum Necessary Standard
69
+
70
+ **Principle:** Use, disclose, and request only the minimum PHI necessary to accomplish purpose.
71
+
72
+ **Exceptions:**
73
+ - Treatment purposes (providers need full information)
74
+ - Patient-authorized disclosures
75
+ - Required by law
76
+
77
+ **Implementation:**
78
+ - Role-based access controls
79
+ - Purpose-specific disclosures
80
+ - Limited data sets when feasible
81
+
82
+ ### Patient Authorization
83
+
84
+ **When required:**
85
+ - Uses/disclosures beyond treatment, payment, operations (TPO)
86
+ - Marketing purposes
87
+ - Sale of PHI
88
+ - Psychotherapy notes
89
+ - Research (unless waiver obtained)
90
+
91
+ **Required elements of authorization:**
92
+ - Specific description of PHI to be used/disclosed
93
+ - Person(s) authorized to make disclosure
94
+ - Person(s) to receive information
95
+ - Purpose of disclosure
96
+ - Expiration date or event
97
+ - Patient signature and date
98
+ - Right to revoke
99
+ - Potential for re-disclosure by recipient
100
+
101
+ ### HIPAA Security Rule (Electronic PHI)
102
+
103
+ **Administrative Safeguards:**
104
+ - Security management process
105
+ - Workforce security
106
+ - Information access management
107
+ - Security awareness and training
108
+ - Security incident procedures
109
+
110
+ **Physical Safeguards:**
111
+ - Facility access controls
112
+ - Workstation use and security
113
+ - Device and media controls
114
+
115
+ **Technical Safeguards:**
116
+ - Access control
117
+ - Audit controls
118
+ - Integrity controls
119
+ - Transmission security
120
+
121
+ ### Breach Notification Rule
122
+
123
+ **Breach definition:** Unauthorized acquisition, access, use, or disclosure of PHI that compromises security or privacy.
124
+
125
+ **Notification requirements:**
126
+ - **Individual notification:** Without unreasonable delay, no later than 60 days
127
+ - **Media notification:** If breach affects >500 residents of a state or jurisdiction
128
+ - **HHS notification:** Within 60 days if >500 individuals; annually if <500
129
+ - **Business associate notification to covered entity:** Without unreasonable delay
130
+
131
+ **Content of notification:**
132
+ - Description of breach
133
+ - Types of information involved
134
+ - Steps individuals should take to protect themselves
135
+ - What entity is doing to investigate/mitigate
136
+ - Contact procedures for questions
137
+
138
+ ### Penalties for HIPAA Violations
139
+
140
+ **Civil penalties (per violation):**
141
+ - Tier 1: $100-$50,000 (unknowing)
142
+ - Tier 2: $1,000-$50,000 (reasonable cause)
143
+ - Tier 3: $10,000-$50,000 (willful neglect, corrected)
144
+ - Tier 4: $50,000-$1.9M (willful neglect, not corrected)
145
+
146
+ **Criminal penalties:**
147
+ - Knowingly obtaining PHI: Up to $50,000 and/or 1 year
148
+ - Under false pretenses: Up to $100,000 and/or 5 years
149
+ - Intent to sell/transfer/use for commercial advantage: Up to $250,000 and/or 10 years
150
+
151
+ ### Research and HIPAA
152
+
153
+ **HIPAA authorization for research:**
154
+ - Specific to research study
155
+ - Describes PHI to be used
156
+ - States that PHI may not be necessary for treatment
157
+
158
+ **Waiver of authorization:**
159
+ - IRB or Privacy Board approval
160
+ - Minimal risk to privacy
161
+ - Research could not practically be conducted without waiver
162
+ - Research could not practically be conducted without access to PHI
163
+ - Plan to protect identifiers
164
+ - Plan to destroy identifiers when appropriate
165
+ - Written assurances
166
+
167
+ **Limited data sets:**
168
+ - Remove 16 of 18 identifiers (may keep dates and geographic subdivisions)
169
+ - Data use agreement required
170
+ - Only for research, public health, or healthcare operations
171
+
172
+ ## 21 CFR Part 11 (Electronic Records and Electronic Signatures)
173
+
174
+ ### Scope
175
+
176
+ FDA regulation establishing criteria for electronic records and electronic signatures to be considered trustworthy, reliable, and equivalent to paper records.
177
+
178
+ **Applies to:**
179
+ - Clinical trial data
180
+ - Regulatory submissions
181
+ - Manufacturing records
182
+ - Laboratory records
183
+ - Any record required by FDA regulations
184
+
185
+ ### Electronic Records Requirements
186
+
187
+ **System validation:**
188
+ - Validation documentation
189
+ - Accuracy, reliability, consistent performance
190
+ - Ability to discern invalid or altered records
191
+
192
+ **Audit trails:**
193
+ - Secure, computer-generated, time-stamped audit trail
194
+ - Record of:
195
+ - Date and time of entry/modification
196
+ - User making change
197
+ - Previous values changed
198
+ - Cannot be modified or deleted by users
199
+ - Retained for records retention period
200
+
201
+ **Operational checks:**
202
+ - Authority checks (user authorization)
203
+ - Device checks (valid input devices)
204
+ - Education and training
205
+ - Confirmation of intent (e.g., "Are you sure?")
206
+
207
+ **Record retention:**
208
+ - Electronic copies as accurate as paper
209
+ - Protection from loss (backups)
210
+ - Protection from unauthorized access
211
+ - Ability to produce readable copies for FDA inspection
212
+
213
+ ### Electronic Signatures Requirements
214
+
215
+ **General requirements:**
216
+ - Unique to one individual
217
+ - Not reused or reassigned
218
+ - Verification of identity before establishing
219
+ - Certification to FDA that electronic signatures are legally binding
220
+
221
+ **Components:**
222
+ - Unique ID
223
+ - Password or biometric
224
+ - Two distinct components when executed
225
+
226
+ **Controls:**
227
+ - Session timeout for inactivity
228
+ - Periodic password changes
229
+ - Prevention of password reuse
230
+ - Detection and reporting of unauthorized use
231
+ - Secure storage of passwords
232
+ - Unique electronic signatures (not shared)
233
+
234
+ **Electronic signature manifestations:**
235
+ Must include:
236
+ - Printed name of signer
237
+ - Date and time of signing
238
+ - Meaning of signature (e.g., review, approval, authorship)
239
+
240
+ ### Closed vs. Open Systems
241
+
242
+ **Closed system:**
243
+ - Access limited to authorized individuals
244
+ - Within a single organization
245
+ - Less stringent requirements
246
+
247
+ **Open system:**
248
+ - Not controlled by persons responsible for content
249
+ - Accessible to unauthorized persons
250
+ - Requires additional measures:
251
+ - Encryption
252
+ - Digital signatures
253
+ - Other authentication/security measures
254
+
255
+ ### Hybrid Systems (Paper + Electronic)
256
+
257
+ **Requirements:**
258
+ - Clear procedures for hybrid system use
259
+ - Maintain record integrity
260
+ - Paper records linked to electronic
261
+ - Cannot delete electronic records after printing
262
+ - Must preserve audit trails
263
+
264
+ ### Legacy Systems
265
+
266
+ **Grandfather clause:**
267
+ - Systems in use before August 20, 1997 may be grandfathered
268
+ - Must demonstrate trustworthiness without full Part 11 compliance
269
+ - Must validate and document reliability
270
+ - Should have migration plan to compliant system
271
+
272
+ ## ICH-GCP (Good Clinical Practice)
273
+
274
+ ### Overview
275
+
276
+ International ethical and scientific quality standard for designing, conducting, recording, and reporting trials involving human subjects.
277
+
278
+ **Purpose:**
279
+ - Protect rights, safety, and well-being of trial subjects
280
+ - Ensure credibility of clinical trial data
281
+
282
+ **Regulatory adoption:**
283
+ - FDA recognizes ICH-GCP (E6)
284
+ - Required for studies supporting regulatory submissions
285
+
286
+ ### Principles of ICH-GCP
287
+
288
+ **1. Ethics:** Clinical trials should be conducted in accordance with ethical principles (Declaration of Helsinki, local laws)
289
+
290
+ **2. Risk-benefit:** Trials should be scientifically sound with favorable risk-benefit ratio
291
+
292
+ **3. Rights and welfare:** Rights, safety, and well-being of subjects take precedence over science and society
293
+
294
+ **4. Available information:** Trials should use available nonclinical and clinical information
295
+
296
+ **5. Quality:** Trials should be scientifically sound and described in clear, detailed protocol
297
+
298
+ **6. Compliance:** Trials should comply with approved protocol
299
+
300
+ **7. Qualified personnel:** Trials should be conducted by qualified individuals
301
+
302
+ **8. Informed consent:** Freely given informed consent should be obtained from each subject
303
+
304
+ **9. Privacy:** Confidentiality of subject records must be protected
305
+
306
+ **10. Quality assurance:** Systems with procedures ensuring quality of data generated
307
+
308
+ **11. Investigational products:** Manufactured, handled, and stored per GMP; used per approved protocol
309
+
310
+ **12. Documentation:** Documentation systems should allow accurate reporting, interpretation, and verification
311
+
312
+ **13. Quality management:** Sponsor should implement quality management system
313
+
314
+ ### Essential Documents
315
+
316
+ **Before trial initiation:**
317
+ - Investigator's Brochure
318
+ - Protocol and amendments
319
+ - Sample CRF
320
+ - IRB/IEC approval
321
+ - Informed consent forms
322
+ - Financial disclosure
323
+ - Curriculum vitae of investigators
324
+ - Normal laboratory values
325
+ - Certifications (lab, equipment)
326
+ - Decoding procedures for blinded trials
327
+ - Monitoring plan
328
+ - Sample labels
329
+ - Instructions for handling investigational products
330
+
331
+ **During trial:**
332
+ - Updates to investigator's brochure
333
+ - Protocol amendments and approvals
334
+ - Continuing IRB review
335
+ - Informed consent updates
336
+ - Curriculum vitae updates
337
+ - Monitoring visit reports
338
+ - Source documents
339
+ - Signed/dated consent forms
340
+ - CRFs
341
+ - Correspondence with regulatory authorities
342
+
343
+ **After trial:**
344
+ - Final report
345
+ - Documentation of investigational product destruction
346
+ - Samples of labels and labeling
347
+ - Post-study access to investigational product (if applicable)
348
+
349
+ ### Investigator Responsibilities
350
+
351
+ **Qualifications:**
352
+ - Qualified by education, training, and experience
353
+ - Has adequate resources
354
+ - Has adequate time
355
+ - Has access to subjects
356
+
357
+ **Compliance:**
358
+ - Conduct trial per protocol
359
+ - Obtain IRB approval before trial
360
+ - Obtain informed consent
361
+ - Report adverse events
362
+ - Maintain essential documents
363
+ - Allow monitoring and auditing
364
+ - Retain records
365
+
366
+ **Safety reporting:**
367
+ - Immediately report SAEs to sponsor
368
+ - Report to IRB per requirements
369
+ - Report to regulatory authority per requirements
370
+
371
+ ### Source Documentation
372
+
373
+ **Source documents:**
374
+ - Original documents, data, and records
375
+ - Examples: hospital records, clinical charts, laboratory notes, ECGs, pharmacy records
376
+ - Must support data in CRFs
377
+
378
+ **Source data verification (SDV):**
379
+ - Comparison of CRF data to source documents
380
+ - Required by monitors
381
+ - Can be 100% or risk-based sampling
382
+
383
+ **Good documentation practice:**
384
+ - Contemporaneous (record in real-time or soon after)
385
+ - Legible
386
+ - Indelible
387
+ - Original (or certified copy)
388
+ - Accurate
389
+ - Complete
390
+ - Attributable (signed/initialed and dated)
391
+ - Not retrospectively changed without documentation
392
+
393
+ **Corrections to source:**
394
+ - Single line through error
395
+ - Reason for change
396
+ - Date and initials
397
+ - Original entry still legible
398
+ - Never use correction fluid/whiteout
399
+ - Never obliterate original entry
400
+
401
+ ### Record Retention
402
+
403
+ **Minimum retention:**
404
+ - 2 years after last approval of marketing application (US)
405
+ - At least 2 years after formal discontinuation of clinical development
406
+ - Longer if required by local regulations
407
+ - 25 years for some countries (e.g., Japan for new drugs)
408
+
409
+ **Documents to retain:**
410
+ - Protocols and amendments
411
+ - CRFs
412
+ - Source documents
413
+ - Signed informed consents
414
+ - IRB correspondence
415
+ - Monitoring reports
416
+ - Audit certificates
417
+ - Regulatory correspondence
418
+ - Final study report
419
+
420
+ ## FDA Regulations
421
+
422
+ ### 21 CFR Part 50 (Informed Consent)
423
+
424
+ **Elements of informed consent:**
425
+ 1. Statement that study involves research
426
+ 2. Description of purpose, duration, procedures
427
+ 3. Experimental procedures identified
428
+ 4. Reasonably foreseeable risks or discomforts
429
+ 5. Benefits to subject or others
430
+ 6. Alternative procedures or treatments
431
+ 7. Confidentiality protections
432
+ 8. Compensation and treatments for injury (if >minimal risk)
433
+ 9. Who to contact for questions
434
+ 10. Statement that participation is voluntary
435
+ 11. Statement that refusal will involve no penalty or loss of benefits
436
+ 12. Statement that subject may discontinue at any time
437
+
438
+ **Additional elements (when appropriate):**
439
+ - Unforeseeable risks to subject or embryo/fetus
440
+ - Circumstances of study termination by investigator
441
+ - Additional costs to subject
442
+ - Consequences of withdrawal
443
+ - New findings that may affect willingness to participate
444
+ - Approximate number of subjects
445
+
446
+ **Documentation:**
447
+ - Written consent required (unless waived)
448
+ - Copy provided to subject
449
+ - Subject or legally authorized representative must sign
450
+ - Person obtaining consent must sign
451
+ - Date of consent
452
+
453
+ **Vulnerable populations:**
454
+ - Children: Parental permission + assent (if capable)
455
+ - Prisoners: Additional protections
456
+ - Pregnant women: Additional protections for fetus
457
+ - Cognitively impaired: Legal representative consent
458
+
459
+ ### 21 CFR Part 56 (IRB Standards)
460
+
461
+ **IRB composition:**
462
+ - At least 5 members
463
+ - Varying backgrounds
464
+ - At least one scientist
465
+ - At least one non-scientist
466
+ - At least one member not affiliated with institution
467
+ - No member may participate in review of study in which member has conflicting interest
468
+
469
+ **IRB review criteria:**
470
+ - Risks minimized
471
+ - Risks reasonable in relation to benefits
472
+ - Selection of subjects equitable
473
+ - Informed consent obtained and documented
474
+ - Data monitoring when appropriate
475
+ - Privacy and confidentiality protected
476
+ - Additional safeguards for vulnerable populations
477
+
478
+ **IRB review types:**
479
+ - Full board review
480
+ - Expedited review (certain categories of minimal risk)
481
+ - Exempt (certain categories)
482
+
483
+ **Continuing review:**
484
+ - At least annually
485
+ - More frequent if determined by IRB
486
+ - Review of progress, new information, consent process
487
+
488
+ **Documentation:**
489
+ - Written procedures
490
+ - Meeting minutes
491
+ - Review determinations
492
+ - Correspondence
493
+ - Retention of records for 3 years
494
+
495
+ ### 21 CFR Part 312 (IND Regulations)
496
+
497
+ **IND requirements:**
498
+ - Investigator's Brochure
499
+ - Protocol(s)
500
+ - Chemistry, manufacturing, and controls information
501
+ - Pharmacology and toxicology information
502
+ - Previous human experience
503
+ - Additional information (if applicable)
504
+
505
+ **IND amendments:**
506
+ - Protocol amendments
507
+ - Information amendments
508
+ - Safety reports
509
+ - Annual reports
510
+
511
+ **Safety reporting:**
512
+ - IND safety reports (7-day and 15-day)
513
+ - Fatal or life-threatening unexpected: 7 days (preliminary), 15 days (complete)
514
+ - Other serious unexpected: 15 days
515
+ - Annual safety reports
516
+
517
+ **General investigational plan:**
518
+ - Rationale for drug or study
519
+ - Indications to be studied
520
+ - Approach to evaluating drug
521
+ - Kinds of trials planned (Phase 1, 2, 3)
522
+ - Estimated duration of study
523
+
524
+ ## EU Clinical Trials Regulation (CTR)
525
+
526
+ **EU CTR 536/2014** (replaced Clinical Trials Directive 2001/20/EC)
527
+
528
+ **Key requirements:**
529
+ - Single submission portal (CTIS - Clinical Trials Information System)
530
+ - Single assessment by multiple member states
531
+ - Transparency requirements (EudraCT database)
532
+ - Public disclosure of clinical trial results
533
+ - Layperson summary of results required
534
+
535
+ **Timelines:**
536
+ - Assessment: 60 days (Part I), additional time for Part II
537
+ - Substantial modifications: 38 days
538
+ - Safety reporting: Within specified timelines to EudraVigilance
539
+
540
+ ## Good Documentation Practice (GDP)
541
+
542
+ ### Principles
543
+
544
+ **ALCOA-CCEA:**
545
+ - **A**ttributable: Who performed action and when
546
+ - **L**egible: Readable and permanent
547
+ - **C**ontemporaneous: Recorded when performed
548
+ - **O**riginal: First capture of information (or certified copy)
549
+ - **A**ccurate: Correct and truthful
550
+
551
+ Additional:
552
+ - **C**omplete: All data captured
553
+ - **C**onsistent: Chronological sequence, no discrepancies
554
+ - **E**nduring: Durable throughout retention period
555
+ - **A**vailable: Accessible for review when needed
556
+
557
+ ### Data Integrity
558
+
559
+ **MHRA (UK) data integrity guidance:**
560
+ - Data governance (ownership, quality)
561
+ - Risk assessment
562
+ - Change management
563
+ - Training
564
+ - Regular audit
565
+
566
+ **Common data integrity issues:**
567
+ - Back-dating of records
568
+ - Deletion or hiding of data
569
+ - Repeat testing without documentation
570
+ - Transcription errors
571
+ - Missing metadata
572
+ - Inadequate audit trails
573
+
574
+ ---
575
+
576
+ This reference provides comprehensive guidance for regulatory compliance in clinical reports and clinical trials, including HIPAA, FDA regulations, ICH-GCP, and EU requirements. Ensure all clinical documentation adheres to applicable regulations.
577
+