scientific-writer 2.3.1__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.
- scientific_writer/.claude/WRITER.md +822 -0
- scientific_writer/.claude/settings.local.json +30 -0
- scientific_writer/.claude/skills/citation-management/SKILL.md +1046 -0
- scientific_writer/.claude/skills/citation-management/assets/bibtex_template.bib +264 -0
- scientific_writer/.claude/skills/citation-management/assets/citation_checklist.md +386 -0
- scientific_writer/.claude/skills/citation-management/references/bibtex_formatting.md +908 -0
- scientific_writer/.claude/skills/citation-management/references/citation_validation.md +794 -0
- scientific_writer/.claude/skills/citation-management/references/google_scholar_search.md +725 -0
- scientific_writer/.claude/skills/citation-management/references/metadata_extraction.md +870 -0
- scientific_writer/.claude/skills/citation-management/references/pubmed_search.md +839 -0
- scientific_writer/.claude/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
- scientific_writer/.claude/skills/citation-management/scripts/extract_metadata.py +569 -0
- scientific_writer/.claude/skills/citation-management/scripts/format_bibtex.py +349 -0
- scientific_writer/.claude/skills/citation-management/scripts/search_google_scholar.py +282 -0
- scientific_writer/.claude/skills/citation-management/scripts/search_pubmed.py +398 -0
- scientific_writer/.claude/skills/citation-management/scripts/validate_citations.py +497 -0
- scientific_writer/.claude/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +641 -0
- scientific_writer/.claude/skills/clinical-reports/README.md +236 -0
- scientific_writer/.claude/skills/clinical-reports/SKILL.md +1088 -0
- scientific_writer/.claude/skills/clinical-reports/assets/case_report_template.md +352 -0
- scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
- scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
- scientific_writer/.claude/skills/clinical-reports/assets/consult_note_template.md +305 -0
- scientific_writer/.claude/skills/clinical-reports/assets/discharge_summary_template.md +453 -0
- scientific_writer/.claude/skills/clinical-reports/assets/hipaa_compliance_checklist.md +395 -0
- scientific_writer/.claude/skills/clinical-reports/assets/history_physical_template.md +305 -0
- scientific_writer/.claude/skills/clinical-reports/assets/lab_report_template.md +309 -0
- scientific_writer/.claude/skills/clinical-reports/assets/pathology_report_template.md +249 -0
- scientific_writer/.claude/skills/clinical-reports/assets/quality_checklist.md +338 -0
- scientific_writer/.claude/skills/clinical-reports/assets/radiology_report_template.md +318 -0
- scientific_writer/.claude/skills/clinical-reports/assets/soap_note_template.md +253 -0
- scientific_writer/.claude/skills/clinical-reports/references/case_report_guidelines.md +570 -0
- scientific_writer/.claude/skills/clinical-reports/references/clinical_trial_reporting.md +693 -0
- scientific_writer/.claude/skills/clinical-reports/references/data_presentation.md +530 -0
- scientific_writer/.claude/skills/clinical-reports/references/diagnostic_reports_standards.md +629 -0
- scientific_writer/.claude/skills/clinical-reports/references/medical_terminology.md +588 -0
- scientific_writer/.claude/skills/clinical-reports/references/patient_documentation.md +744 -0
- scientific_writer/.claude/skills/clinical-reports/references/peer_review_standards.md +585 -0
- scientific_writer/.claude/skills/clinical-reports/references/regulatory_compliance.md +577 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/check_deidentification.py +346 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/compliance_checker.py +78 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/extract_clinical_data.py +102 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/format_adverse_events.py +103 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/generate_report_template.py +163 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/terminology_validator.py +133 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/validate_case_report.py +334 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/validate_trial_report.py +89 -0
- scientific_writer/.claude/skills/document-skills/docx/LICENSE.txt +30 -0
- scientific_writer/.claude/skills/document-skills/docx/SKILL.md +197 -0
- scientific_writer/.claude/skills/document-skills/docx/docx-js.md +350 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +75 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/pack.py +159 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/unpack.py +29 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/base.py +951 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/docx.py +274 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +315 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +279 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml.md +610 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/__init__.py +1 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/document.py +1276 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/templates/comments.xml +3 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtended.xml +3 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +3 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsIds.xml +3 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/templates/people.xml +3 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/utilities.py +374 -0
- scientific_writer/.claude/skills/document-skills/pdf/LICENSE.txt +30 -0
- scientific_writer/.claude/skills/document-skills/pdf/SKILL.md +294 -0
- scientific_writer/.claude/skills/document-skills/pdf/forms.md +205 -0
- scientific_writer/.claude/skills/document-skills/pdf/reference.md +612 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes.py +70 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +226 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/check_fillable_fields.py +12 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +35 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/create_validation_image.py +41 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/extract_form_field_info.py +152 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_fillable_fields.py +114 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +108 -0
- scientific_writer/.claude/skills/document-skills/pptx/LICENSE.txt +30 -0
- scientific_writer/.claude/skills/document-skills/pptx/SKILL.md +484 -0
- scientific_writer/.claude/skills/document-skills/pptx/html2pptx.md +625 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd +75 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/pack.py +159 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/unpack.py +29 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validate.py +69 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/__init__.py +15 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/base.py +951 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/docx.py +274 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/pptx.py +315 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/redlining.py +279 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml.md +427 -0
- scientific_writer/.claude/skills/document-skills/pptx/scripts/html2pptx.js +979 -0
- scientific_writer/.claude/skills/document-skills/pptx/scripts/inventory.py +1020 -0
- scientific_writer/.claude/skills/document-skills/pptx/scripts/rearrange.py +231 -0
- scientific_writer/.claude/skills/document-skills/pptx/scripts/replace.py +385 -0
- scientific_writer/.claude/skills/document-skills/pptx/scripts/thumbnail.py +450 -0
- scientific_writer/.claude/skills/document-skills/xlsx/LICENSE.txt +30 -0
- scientific_writer/.claude/skills/document-skills/xlsx/SKILL.md +289 -0
- scientific_writer/.claude/skills/document-skills/xlsx/recalc.py +178 -0
- scientific_writer/.claude/skills/hypothesis-generation/SKILL.md +155 -0
- scientific_writer/.claude/skills/hypothesis-generation/assets/hypothesis_output_template.md +302 -0
- scientific_writer/.claude/skills/hypothesis-generation/references/experimental_design_patterns.md +327 -0
- scientific_writer/.claude/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +196 -0
- scientific_writer/.claude/skills/hypothesis-generation/references/literature_search_strategies.md +505 -0
- scientific_writer/.claude/skills/latex-posters/README.md +417 -0
- scientific_writer/.claude/skills/latex-posters/SKILL.md +919 -0
- scientific_writer/.claude/skills/latex-posters/assets/baposter_template.tex +257 -0
- scientific_writer/.claude/skills/latex-posters/assets/beamerposter_template.tex +244 -0
- scientific_writer/.claude/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
- scientific_writer/.claude/skills/latex-posters/assets/tikzposter_template.tex +251 -0
- scientific_writer/.claude/skills/latex-posters/references/latex_poster_packages.md +745 -0
- scientific_writer/.claude/skills/latex-posters/references/poster_content_guide.md +748 -0
- scientific_writer/.claude/skills/latex-posters/references/poster_design_principles.md +806 -0
- scientific_writer/.claude/skills/latex-posters/references/poster_layout_design.md +900 -0
- scientific_writer/.claude/skills/latex-posters/scripts/review_poster.sh +214 -0
- scientific_writer/.claude/skills/literature-review/SKILL.md +546 -0
- scientific_writer/.claude/skills/literature-review/assets/review_template.md +412 -0
- scientific_writer/.claude/skills/literature-review/references/citation_styles.md +166 -0
- scientific_writer/.claude/skills/literature-review/references/database_strategies.md +381 -0
- scientific_writer/.claude/skills/literature-review/scripts/generate_pdf.py +176 -0
- scientific_writer/.claude/skills/literature-review/scripts/search_databases.py +303 -0
- scientific_writer/.claude/skills/literature-review/scripts/verify_citations.py +222 -0
- scientific_writer/.claude/skills/markitdown/INSTALLATION_GUIDE.md +318 -0
- scientific_writer/.claude/skills/markitdown/LICENSE.txt +22 -0
- scientific_writer/.claude/skills/markitdown/OPENROUTER_INTEGRATION.md +359 -0
- scientific_writer/.claude/skills/markitdown/QUICK_REFERENCE.md +309 -0
- scientific_writer/.claude/skills/markitdown/README.md +184 -0
- scientific_writer/.claude/skills/markitdown/SKILL.md +450 -0
- scientific_writer/.claude/skills/markitdown/SKILL_SUMMARY.md +307 -0
- scientific_writer/.claude/skills/markitdown/assets/example_usage.md +463 -0
- scientific_writer/.claude/skills/markitdown/references/api_reference.md +399 -0
- scientific_writer/.claude/skills/markitdown/references/file_formats.md +542 -0
- scientific_writer/.claude/skills/markitdown/scripts/batch_convert.py +228 -0
- scientific_writer/.claude/skills/markitdown/scripts/convert_literature.py +283 -0
- scientific_writer/.claude/skills/markitdown/scripts/convert_with_ai.py +243 -0
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% Professional guidelines for treatment plan documentation
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% Last updated: 2025
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# Treatment Plan Standards
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## Overview
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Treatment plans are comprehensive documents that outline systematic approaches to addressing patient health conditions through evidence-based interventions, measurable goals, and structured follow-up. This reference provides professional standards, documentation requirements, and legal considerations for creating high-quality treatment plans across all medical specialties.
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## Core Documentation Standards
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### 1. Executive Summary Best Practices (Foundation Medicine Model)
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**CRITICAL: All treatment plans MUST include a prominent "Treatment Plan Highlights" summary box on the first page.**
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Following the Foundation Medicine model for genomic profiling reports, treatment plans should begin with a concise, bulletin-style summary that provides immediate access to key actionable information:
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**Components of Treatment Plan Highlights Box:**
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- **Key Diagnosis**: Primary condition with ICD-10 code, severity/stage (1 line)
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- **Primary Treatment Goals**: 2-3 SMART goals in bullet format
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- **Main Interventions**: 2-3 key interventions (pharmacological, non-pharmacological, monitoring)
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- **Timeline Overview**: Brief treatment duration/phases (1 line)
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**Format Requirements:**
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- Use colored box (tcolorbox in LaTeX) to make it visually prominent
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- Place immediately after title, before Patient Information section
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- Summary must fit on first page with patient demographics
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- Use concise, actionable language
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- Focus on what clinicians need to know immediately
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**Optimal Document Length:**
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- **Preferred**: 1 page for most treatment plans (quick-reference format)
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- **Standard**: 3-4 pages for moderate complexity cases
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- **Extended**: 5-6 pages maximum for highly complex cases only
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- Prioritize brevity, clarity, and actionability over comprehensive detail
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- Think "clinical decision support card" not "comprehensive textbook"
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**Design Philosophy:**
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The highlights box enables efficient clinical decision-making by providing critical information upfront, following evidence-based practices from precision medicine reporting. This approach improves care coordination, reduces time to treatment initiation, and ensures key information is never overlooked.
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### 2. Essential Components
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All treatment plans must include:
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#### Patient Information (De-identified for Sharing)
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- Unique patient identifier (not name or MRN)
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- Age range (not exact birth date)
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- Relevant demographics
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- Date of plan creation
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- Provider name and credentials
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- HIPAA compliance statement
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#### Diagnosis and Assessment
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- Primary diagnosis with ICD-10 code
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- Secondary diagnoses and comorbidities
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- Severity classification or staging
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- Functional assessment and baseline status
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- Risk stratification
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- Prognostic considerations
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#### Treatment Goals (SMART Format)
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- **Specific**: Clearly defined outcomes
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- **Measurable**: Quantifiable metrics or observable criteria
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- **Achievable**: Realistic given patient circumstances
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- **Relevant**: Aligned with patient values and priorities
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- **Time-bound**: Defined timeframe for achievement
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Short-term goals (weeks to 3 months) and long-term goals (3-12+ months) should be distinguished.
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#### Interventions
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- **Pharmacological**: Specific medications, doses, frequencies, rationales
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- **Non-pharmacological**: Lifestyle modifications, behavioral interventions, education
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- **Procedural**: Planned procedures, specialist referrals, diagnostic testing
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#### Timeline and Schedule
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- Treatment phases with durations
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- Appointment frequency
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- Milestone assessments
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- Expected treatment duration
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#### Monitoring Parameters
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- Clinical outcomes to track
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- Assessment tools and scales
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- Monitoring frequency
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- Intervention thresholds
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#### Expected Outcomes
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- Primary outcome measures
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- Success criteria
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- Timeline for improvement
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- Criteria for treatment modification
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#### Follow-up Plan
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- Scheduled appointments
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- Communication protocols
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- Emergency procedures
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- Transition planning
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#### Patient Education
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- Condition understanding
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- Self-management skills
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- Warning signs
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- Resources and support
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#### Risk Mitigation
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- Potential adverse effects
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- Safety monitoring
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- Emergency action plans
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- Complication prevention
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### 2. Professional Documentation Standards
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#### Clarity and Precision
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- Use professional medical terminology appropriately
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- Define abbreviations on first use
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- Avoid ambiguous language
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- Specific rather than vague descriptions
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**Good Example**: "Reduce HbA1c from 8.5% to <7% within 3 months"
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**Poor Example**: "Improve diabetes control"
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#### Completeness
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- Address all relevant aspects of condition
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- Include rationale for treatment choices
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- Document shared decision-making
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- Address patient preferences and concerns
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#### Accuracy
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- Factually correct information
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- Current evidence-based recommendations
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- Appropriate dosing and frequencies
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- Correct ICD-10 and CPT codes
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#### Timeliness
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- Plans created at diagnosis or treatment initiation
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- Updated after significant clinical changes
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- Regular scheduled updates (quarterly to annually)
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- Dated and signed promptly
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#### Legibility and Organization
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- Professional formatting
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- Logical flow and structure
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- Consistent use of headings and sections
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- Easy to locate key information
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### 3. Legal and Regulatory Requirements
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#### Medical Necessity Documentation
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Treatment plans must demonstrate:
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- Appropriateness of interventions for diagnosis
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- Evidence supporting treatment choices
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- Expected outcomes justify costs and risks
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- Frequency and duration are reasonable
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- Less invasive options considered
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#### Informed Consent Documentation
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Record that patient:
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- Understands diagnosis and prognosis
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- Aware of treatment options, risks, and benefits
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- Knows alternatives to proposed treatment
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- Had opportunity to ask questions
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- Voluntarily agrees to treatment plan
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#### Privacy and Confidentiality (HIPAA)
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- Protected Health Information (PHI) safeguarded
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- De-identification for sharing:
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- Remove 18 HIPAA identifiers per Safe Harbor method
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- Names, dates (except year), geographic subdivisions smaller than state
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- Contact information (phone, fax, email, addresses)
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- Social Security numbers, medical record numbers, account numbers
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- Biometric identifiers, photos, other unique identifiers
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- Access limited to those with treatment, payment, or operations need
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- Patient authorization for non-routine disclosures
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#### Billing and Reimbursement Support
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- ICD-10 diagnosis codes for all conditions
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- CPT codes for procedures
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- Documentation of medical necessity
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- Justification for level of service
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- Compliance with payer-specific requirements
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#### Quality Measure Reporting
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Enable extraction of quality metrics:
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- HEDIS measures (diabetes HbA1c testing, BP control, etc.)
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- CMS quality reporting (MIPS, ACO measures)
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- Disease-specific quality indicators
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- Patient safety indicators
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#### Liability Protection
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Defensible documentation includes:
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- Rationale for clinical decisions
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- Consideration of differential diagnosis
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- Risk-benefit analysis
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- Patient education and warnings
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- Follow-up plan for abnormal findings
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- Addressing non-adherence or patient refusal
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## Professional Practice Standards
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### Joint Commission Standards
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#### Patient-Centered Care
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- Treatment plans developed with patient participation
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- Goals reflect patient values and preferences
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- Cultural and linguistic needs addressed
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- Health literacy appropriate communication
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#### Multidisciplinary Coordination
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- Input from relevant disciplines
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- Clear role delineation
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- Communication among team members
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- Coordinated interventions
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#### Evidence-Based Practice
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- Interventions based on current evidence
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- Clinical practice guidelines followed
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- Variation from guidelines documented and justified
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- Literature supports treatment choices
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### Commission on Accreditation of Rehabilitation Facilities (CARF)
|
|
222
|
+
|
|
223
|
+
For rehabilitation treatment plans:
|
|
224
|
+
- Individualized based on comprehensive assessment
|
|
225
|
+
- Measurable, achievable, time-specific goals
|
|
226
|
+
- Regular team review and modification
|
|
227
|
+
- Patient and family involvement
|
|
228
|
+
- Transition and discharge planning
|
|
229
|
+
|
|
230
|
+
### Centers for Medicare & Medicaid Services (CMS)
|
|
231
|
+
|
|
232
|
+
#### Conditions of Participation
|
|
233
|
+
- Physician orders for treatment
|
|
234
|
+
- Periodic review and revision
|
|
235
|
+
- Progress toward goals documented
|
|
236
|
+
- Care plan accessible to all team members
|
|
237
|
+
|
|
238
|
+
#### Documentation Requirements
|
|
239
|
+
- Legible (typed or clear handwriting)
|
|
240
|
+
- Dated and authenticated (signed)
|
|
241
|
+
- Amendments/corrections properly marked
|
|
242
|
+
- Retention per state law (typically 7-10 years, longer for minors)
|
|
243
|
+
|
|
244
|
+
## Medical Specialty Standards
|
|
245
|
+
|
|
246
|
+
### Primary Care
|
|
247
|
+
- Annual comprehensive assessment and plan update
|
|
248
|
+
- Chronic disease management protocols
|
|
249
|
+
- Preventive care integration
|
|
250
|
+
- Medication reconciliation
|
|
251
|
+
- Care coordination with specialists
|
|
252
|
+
|
|
253
|
+
### Behavioral Health
|
|
254
|
+
- Mental status examination
|
|
255
|
+
- Psychiatric diagnoses per DSM-5 criteria
|
|
256
|
+
- Suicide/homicide risk assessment and safety planning
|
|
257
|
+
- Measurable behavioral outcomes
|
|
258
|
+
- Crisis intervention plan
|
|
259
|
+
- Substance use assessment
|
|
260
|
+
- 42 CFR Part 2 compliance for substance use treatment
|
|
261
|
+
|
|
262
|
+
### Rehabilitation
|
|
263
|
+
- Functional assessments (FIM, Barthel Index, etc.)
|
|
264
|
+
- Activity limitations and participation restrictions
|
|
265
|
+
- Short-term and long-term functional goals
|
|
266
|
+
- Therapy frequency, intensity, duration
|
|
267
|
+
- Home exercise program
|
|
268
|
+
- Assistive devices and DME
|
|
269
|
+
- Discharge criteria
|
|
270
|
+
|
|
271
|
+
### Surgical/Perioperative
|
|
272
|
+
- Indication for surgery documented
|
|
273
|
+
- Preoperative risk assessment (ASA, RCRI)
|
|
274
|
+
- Medical optimization plan
|
|
275
|
+
- Enhanced Recovery After Surgery (ERAS) protocols when applicable
|
|
276
|
+
- Postoperative milestones
|
|
277
|
+
- Discharge criteria and planning
|
|
278
|
+
|
|
279
|
+
### Pain Management
|
|
280
|
+
- Comprehensive pain assessment (location, intensity, quality, temporal pattern, impact)
|
|
281
|
+
- Pain type (nociceptive, neuropathic, mixed)
|
|
282
|
+
- Multimodal analgesia approach
|
|
283
|
+
- Opioid risk assessment (ORT, SOAPP)
|
|
284
|
+
- If opioids: CDC guidelines compliance, treatment agreement, UDS, PDMP
|
|
285
|
+
- Functional goals (not just pain scores)
|
|
286
|
+
- Psychological screening and intervention
|
|
287
|
+
|
|
288
|
+
## Quality Indicators for Treatment Plans
|
|
289
|
+
|
|
290
|
+
### Completeness Metrics
|
|
291
|
+
- All required sections present (100%)
|
|
292
|
+
- Goals meet SMART criteria ($\geq$90%)
|
|
293
|
+
- Interventions have clear rationales ($\geq$95%)
|
|
294
|
+
- Monitoring plan includes frequency ($\geq$95%)
|
|
295
|
+
- Patient education documented (100%)
|
|
296
|
+
|
|
297
|
+
### Clinical Quality Metrics
|
|
298
|
+
- Evidence-based interventions ($\geq$90%)
|
|
299
|
+
- Guideline-concordant care ($\geq$85%)
|
|
300
|
+
- Avoidance of low-value care (100%)
|
|
301
|
+
- Appropriate preventive care included ($\geq$95%)
|
|
302
|
+
|
|
303
|
+
### Patient-Centered Metrics
|
|
304
|
+
- Patient preferences documented ($\geq$90%)
|
|
305
|
+
- Shared decision-making noted ($\geq$85%)
|
|
306
|
+
- Culturally appropriate care (100%)
|
|
307
|
+
- Health literacy addressed ($\geq$90%)
|
|
308
|
+
|
|
309
|
+
### Safety Metrics
|
|
310
|
+
- Risk mitigation strategies present (100%)
|
|
311
|
+
- Medication safety addressed (100%)
|
|
312
|
+
- Emergency procedures documented (100%)
|
|
313
|
+
- Red flags/warning signs communicated (100%)
|
|
314
|
+
|
|
315
|
+
## Common Documentation Deficiencies and Solutions
|
|
316
|
+
|
|
317
|
+
### Problem: Vague Goals
|
|
318
|
+
**Deficiency**: "Improve diabetes"
|
|
319
|
+
**Solution**: "Reduce HbA1c from 8.5% to <7% within 3 months through medication intensification and lifestyle modification"
|
|
320
|
+
|
|
321
|
+
### Problem: Missing Rationales
|
|
322
|
+
**Deficiency**: Lists medications without explanation
|
|
323
|
+
**Solution**: "Metformin 1000mg BID - first-line therapy for T2DM, reduces hepatic glucose production, target dose for HbA1c reduction"
|
|
324
|
+
|
|
325
|
+
### Problem: No Timeline
|
|
326
|
+
**Deficiency**: Goals without timeframes
|
|
327
|
+
**Solution**: "Short-term (3 months): HbA1c <7.5%; Long-term (6 months): HbA1c <7%"
|
|
328
|
+
|
|
329
|
+
### Problem: Incomplete Monitoring
|
|
330
|
+
**Deficiency**: "Monitor labs"
|
|
331
|
+
**Solution**: "HbA1c every 3 months until at goal, then every 6 months; CMP every 6 months to monitor renal function on metformin and ACE inhibitor"
|
|
332
|
+
|
|
333
|
+
### Problem: Absent Patient Education
|
|
334
|
+
**Deficiency**: No documentation of education provided
|
|
335
|
+
**Solution**: Dedicated section documenting: condition education, self-management skills taught, warning signs communicated, resources provided
|
|
336
|
+
|
|
337
|
+
### Problem: Missing Safety Planning
|
|
338
|
+
**Deficiency**: No risk mitigation
|
|
339
|
+
**Solution**: Specific safety concerns addressed (e.g., hypoglycemia risk with insulin, monitoring plan, patient taught recognition and treatment)
|
|
340
|
+
|
|
341
|
+
## Electronic Health Record (EHR) Integration
|
|
342
|
+
|
|
343
|
+
### Structured Data Entry
|
|
344
|
+
- Use templates for consistency
|
|
345
|
+
- Coded diagnoses (ICD-10), procedures (CPT)
|
|
346
|
+
- Structured goals enable outcome tracking
|
|
347
|
+
- Discrete medication fields (name, dose, route, frequency)
|
|
348
|
+
|
|
349
|
+
### Clinical Decision Support
|
|
350
|
+
- Evidence-based order sets
|
|
351
|
+
- Drug-drug interaction alerts
|
|
352
|
+
- Guideline reminders
|
|
353
|
+
- Quality measure tracking
|
|
354
|
+
|
|
355
|
+
### Care Plan Sharing
|
|
356
|
+
- Patient portal access (patient-friendly version)
|
|
357
|
+
- Interoperability standards (C-CDA)
|
|
358
|
+
- Shared with care team
|
|
359
|
+
- Transitions of care summary
|
|
360
|
+
|
|
361
|
+
## Audit and Peer Review
|
|
362
|
+
|
|
363
|
+
### Internal Quality Review
|
|
364
|
+
- Random sample chart audits (e.g., 5% quarterly)
|
|
365
|
+
- Checklist-based review (completeness, quality)
|
|
366
|
+
- Feedback to providers
|
|
367
|
+
- Continuous quality improvement
|
|
368
|
+
|
|
369
|
+
### External Review
|
|
370
|
+
- Payer audits (documentation supports billing)
|
|
371
|
+
- Regulatory surveys (Joint Commission, CMS)
|
|
372
|
+
- Malpractice case review
|
|
373
|
+
- Peer review for privileging/credentialing
|
|
374
|
+
|
|
375
|
+
### Audit Criteria
|
|
376
|
+
- Documentation completeness
|
|
377
|
+
- Clinical appropriateness
|
|
378
|
+
- Regulatory compliance
|
|
379
|
+
- Billing integrity
|
|
380
|
+
- Patient safety
|
|
381
|
+
|
|
382
|
+
## Treatment Plan Revision and Updates
|
|
383
|
+
|
|
384
|
+
### When to Update Treatment Plans
|
|
385
|
+
|
|
386
|
+
**Scheduled Updates**:
|
|
387
|
+
- Chronic disease management: Every 3-6 months minimum
|
|
388
|
+
- Behavioral health: Every 30-90 days depending on acuity
|
|
389
|
+
- Rehabilitation: Weekly to biweekly during active therapy
|
|
390
|
+
- Annual comprehensive update for all chronic conditions
|
|
391
|
+
|
|
392
|
+
**Triggered Updates**:
|
|
393
|
+
- Significant change in clinical status
|
|
394
|
+
- New diagnosis
|
|
395
|
+
- Treatment goals achieved or not progressing
|
|
396
|
+
- Patient request or preference change
|
|
397
|
+
- Hospitalization or emergency department visit
|
|
398
|
+
- Medication changes or adverse events
|
|
399
|
+
|
|
400
|
+
### Documentation of Changes
|
|
401
|
+
- Date of revision
|
|
402
|
+
- Reason for update
|
|
403
|
+
- What changed (goals, interventions, timeline)
|
|
404
|
+
- Provider signature
|
|
405
|
+
- Maintain prior versions for record
|
|
406
|
+
|
|
407
|
+
## Specialty-Specific Requirements
|
|
408
|
+
|
|
409
|
+
### Diabetes Management Plans
|
|
410
|
+
- HbA1c targets individualized
|
|
411
|
+
- Complication screening schedule (eyes, feet, kidneys)
|
|
412
|
+
- Self-monitoring blood glucose frequency
|
|
413
|
+
- Hypoglycemia recognition and treatment
|
|
414
|
+
- Sick day management
|
|
415
|
+
|
|
416
|
+
### Heart Failure Plans
|
|
417
|
+
- GDMT (guideline-directed medical therapy) checklist
|
|
418
|
+
- Volume management (daily weights, fluid/sodium restriction)
|
|
419
|
+
- NYHA functional class documentation
|
|
420
|
+
- Device therapy consideration
|
|
421
|
+
- Hospitalization triggers
|
|
422
|
+
|
|
423
|
+
### Mental Health Treatment Plans
|
|
424
|
+
- DSM-5 diagnostic criteria met
|
|
425
|
+
- Suicide/violence risk assessment
|
|
426
|
+
- Safety planning
|
|
427
|
+
- Psychotherapy modality and frequency
|
|
428
|
+
- Medication trials and responses
|
|
429
|
+
- Functional goals (return to work, relationships)
|
|
430
|
+
|
|
431
|
+
### Chronic Pain Plans
|
|
432
|
+
- Comprehensive pain assessment
|
|
433
|
+
- Functional goals (not just pain scores)
|
|
434
|
+
- Multimodal analgesia
|
|
435
|
+
- Opioid risk assessment if prescribing
|
|
436
|
+
- Physical and psychological interventions
|
|
437
|
+
- Activity modification and pacing
|
|
438
|
+
|
|
439
|
+
## Cultural Competence and Health Equity
|
|
440
|
+
|
|
441
|
+
### Culturally Appropriate Care
|
|
442
|
+
- Recognize cultural health beliefs and practices
|
|
443
|
+
- Address language barriers (interpreter services)
|
|
444
|
+
- Respect religious and cultural preferences in treatment
|
|
445
|
+
- Consider social determinants of health (housing, food security, transportation)
|
|
446
|
+
- Avoid assumptions based on stereotypes
|
|
447
|
+
|
|
448
|
+
### Health Literacy
|
|
449
|
+
- Assess patient understanding (teach-back method)
|
|
450
|
+
- Use plain language, avoid medical jargon
|
|
451
|
+
- Visual aids and written materials at appropriate reading level
|
|
452
|
+
- Tailor education to patient's learning style
|
|
453
|
+
|
|
454
|
+
### Addressing Disparities
|
|
455
|
+
- Screen for social needs and barriers
|
|
456
|
+
- Connect to community resources
|
|
457
|
+
- Culturally tailored interventions when evidence supports
|
|
458
|
+
- Track outcomes by demographic groups, address disparities
|
|
459
|
+
|
|
460
|
+
## References and Guidelines
|
|
461
|
+
|
|
462
|
+
### General Standards
|
|
463
|
+
- Joint Commission Standards Manual
|
|
464
|
+
- CMS Conditions of Participation
|
|
465
|
+
- State medical board documentation requirements
|
|
466
|
+
|
|
467
|
+
### Specialty Guidelines
|
|
468
|
+
- American College of Physicians (ACP)
|
|
469
|
+
- American Academy of Family Physicians (AAFP)
|
|
470
|
+
- American Psychiatric Association (APA)
|
|
471
|
+
- American Physical Therapy Association (APTA)
|
|
472
|
+
- Disease-specific societies (ADA, AHA, ACC, etc.)
|
|
473
|
+
|
|
474
|
+
### Regulatory
|
|
475
|
+
- HIPAA Privacy Rule (45 CFR Part 160, 164)
|
|
476
|
+
- 42 CFR Part 2 (Substance Use Disorder Confidentiality)
|
|
477
|
+
- 21 CFR Part 11 (Electronic Records, applicable for research/trials)
|
|
478
|
+
- State scope of practice laws
|
|
479
|
+
|
|
480
|
+
---
|
|
481
|
+
|
|
482
|
+
**Document Version**: 1.0
|
|
483
|
+
**Last Updated**: January 2025
|
|
484
|
+
**Next Review**: January 2026
|
|
485
|
+
|