clinical-reports

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Malicious tool definition detected

Tool: README.md [2/2] Description: Association (AMA) - American College of Radiology (ACR) - College of American Pathologists (CAP) - Clinical Laboratory Standards Institute (CLSI) - International Council for Harmonisation (ICH) ## Support For issues or questions about the clinical-reports skill: 1.

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Tool: SKILL.md [1/6] Description: --- name: clinical-reports description: "Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries).

Tool: SKILL.md [2/6] Description: (AMA, Vancouver, APA) - Structured vs. unstructured abstract - Supplementary materials policies Check journal instructions for authors before submission. #### De-identification and Privacy **18 HIPAA Identifiers to Remove or Alter:** 1. Names 2.

Tool: SKILL.md [6/6] Description: `scripts/terminology_validator.py` - Validate medical terminology and coding Load these resources as needed when working on specific clinical reports.

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Tool: assets/case_report_template.md [1/2] Description: # Clinical Case Report Template ## Title [Insert descriptive title that includes "Case Report" or "Case Study" and indicates the clinical focus] Example: Unusual Presentation of Acute Appendicitis in an Elderly Patient: A Case Report ## Author Information [Author names, affiliations, ORCID IDs] **Corresponding Author:** [Name] [Email] [Institution] ## Keywords [2-5 keywords, preferably MeSH terms] Example: Appendicitis, Atypical presentatio

Tool: assets/case_report_template.md [2/2] Description: on request.

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Tool: assets/clinical_trial_csr_template.md [1/2] Description: # Clinical Study Report (CSR) Template ## ICH-E3 Format --- # TITLE PAGE **Study Title:** [Full descriptive title including compound, indication, phase] **Protocol Number:** [Sponsor protocol number] **Protocol Version:** [Final protocol version and date] **Sponsor:** [Company name and address] **Compound/Drug Name:** [Generic and proprietary names, compound code] **Indication:** [Therapeutic area and specific indication studied] **S

Tool: assets/clinical_trial_csr_template.md [2/2] Description: 0.05 (two-sided) --- # STUDY PATIENTS (Section 6) ## 6.1 Disposition of Patients **Participant Flow (CONSORT Diagram):** [Include detailed CONSORT diagram showing screening through analysis] **Summary Table:** | Category | Treatment A | Treatment B | Total | |----------|-------------|-------------|-------| | Screened | N | N | N | | Screen failures | N (%) | N (%) | N (%) | | Randomized | N | N | N | | Received treatment | N (%) | N

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Tool: assets/clinical_trial_sae_template.md [1/2] Description: # Serious Adverse Event (SAE) Report Template ## Report Information **Report Type:** [ ] Initial Report [ ] Follow-up Report [ ] Final Report **Report Number:** [SAE-YYYY-####] **Report Date:** [MM/DD/YYYY] **Reporter:** [Name and title] **Reporter Contact:** [Email and phone] **Follow-up Number:** [If follow-up: #1, #2, etc.] **Previous Report Date:** [If follow-up] --- ## Study Information **Protocol Number:** [Protocol ID] **Proto

Tool: assets/clinical_trial_sae_template.md [2/2] Description: | [Range] | [MM/DD] | [Before/During/After] | **Imaging/Diagnostic Studies:** - **[Study type] ([Date]):** [Key findings] **ECG/Monitoring:** [Results if relevant] --- ## Detailed Event Narrative [Comprehensive chronological narrative of the event] **Minimum elements to include:** - Patient demographics and study participation timeline - Relevant medical history - Chronological description of event development - Symptoms, signs, and

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Tool: assets/consult_note_template.md Description: # Consultation Note Template **Patient Name:** [Last, First] **Medical Record Number:** [MRN] **Date of Birth:** [MM/DD/YYYY] **Age/Sex:** [years, M/F] **Consultation Date:** [MM/DD/YYYY] **Consultation Time:** [HH:MM] **Location:** [Floor, Room number] **Requesting Service:** [Primary team] **Requesting Physician:** [Name] **Consulting Service:** [Cardiology, Nephrology, etc.] **Consulting Physician:** [Name and credentials] --- ## Reason for C

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Tool: assets/discharge_summary_template.md [1/2] Description: # Discharge Summary Template ## Patient Information **Patient Name:** [Last, First] **Medical Record Number:** [MRN] **Date of Birth:** [MM/DD/YYYY] **Age:** [years] **Sex:** [M/F] **Admission Date:** [MM/DD/YYYY] **Discharge Date:** [MM/DD/YYYY] **Length of Stay:** [X days] **Admitting Service:** [Medicine/Surgery/Cardiology/etc.] **Attending Physician:** [Name] **Primary Care Physician:** [Name and contact] **Consulting Services:**

Tool: assets/discharge_summary_template.md [2/2] Description: name]: [When due, where to go, reason] - Results will be sent to: [Provider name] ### Referrals Placed - [Specialty]: [Reason for referral, contact information] --- ## Patient Instructions ### Activity - [Specific activity restrictions or recommendations] - Example: "Resume normal activities as tolerated.

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Tool: assets/hipaa_compliance_checklist.md [1/2] Description: # HIPAA Compliance Checklist for Clinical Reports ## 18 HIPAA Identifiers - De-identification Checklist Verify that ALL of the following identifiers have been removed or altered: - [ ] **1.

Tool: assets/hipaa_compliance_checklist.md [2/2] Description: Expert Determination ### Safe Harbor Method - [ ] All 18 identifiers removed - [ ] No actual knowledge that remaining information could identify individual - [ ] Most straightforward method - [ ] Recommended for most clinical reports ### Expert Determination Method - [ ] Qualified statistician/expert determined very small re-identification risk - [ ] Methodology documented - [ ] Analysis methods specified - [ ] Conclusion documented -

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Tool: assets/history_physical_template.md [1/2] Description: # History and Physical Examination (H&P) Template **Patient Name:** [Last, First] **Medical Record Number:** [MRN] **Date of Birth:** [MM/DD/YYYY] **Age:** [years] **Sex:** [M/F] **Date of Admission/Encounter:** [MM/DD/YYYY] **Time:** [HH:MM] **Location:** [Hospital floor, Clinic, ED] **Admitting Service:** [Medicine, Surgery, etc.] **Attending Physician:** [Name] --- ## Chief Complaint (CC) "[Patient's stated reason for seeking care,

Tool: assets/history_physical_template.md [2/2] Description: --- ## Assessment and Plan **Assessment:** [Patient summary statement in one sentence] **Problem List:** **1.

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Tool: assets/lab_report_template.md [1/2] Description: # Laboratory Report Template ## Patient Information **Patient Name:** [Last, First] **Medical Record Number:** [MRN] **Date of Birth:** [MM/DD/YYYY] **Age/Sex:** [Age years, M/F] **Ordering Physician:** [Name] **Location:** [Inpatient unit / Outpatient clinic] --- ## Specimen Information **Specimen Type:** [Blood / Serum / Plasma / Urine / CSF / Other] **Collection Date/Time:** [MM/DD/YYYY at HH:MM] **Received Date/Time:** [MM/DD/YYYY at HH:

Tool: assets/lab_report_template.md [2/2]

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Tool: assets/pathology_report_template.md Description: # Surgical Pathology Report Template ## Patient and Specimen Information **Patient Name:** [Last, First] **Medical Record Number:** [MRN] **Date of Birth:** [MM/DD/YYYY] **Age:** [years] **Sex:** [M/F] **Accession Number:** [PathologyAccessionNumber] **Specimen Received:** [Date and time] **Report Date:** [Date] **Ordering Physician:** [Name] **Clinical Service:** [Department] --- ## Specimen(s) Submitted **Specimen A:** [Description of spec

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Tool: assets/quality_checklist.md [1/2]

Tool: assets/quality_checklist.md [2/2] Description: ] Family history - [ ] Social history - [ ] Review of systems (≥10 systems for comprehensive) - [ ] Complete physical exam (≥8 systems) - [ ] Laboratory and imaging results - [ ] Assessment and plan for each problem - [ ] Code status documented - [ ] Completed within 24 hours of admission - [ ] Signed and cosigned (if required) ### Discharge Summary - [ ] Admission and discharge dates - [ ] Length of stay - [ ] Admission diagnosis - [ ] Discha

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Tool: assets/radiology_report_template.md [1/2] Description: # Radiology Report Template ## Patient Information **Patient Name:** [Last, First] **Medical Record Number:** [MRN] **Date of Birth:** [MM/DD/YYYY] **Age:** [years] **Sex:** [M/F] **Exam Date:** [MM/DD/YYYY] **Exam Time:** [HH:MM] **Accession Number:** [Number] **Referring Physician:** [Name] **Ordering Service:** [Service/Department] --- ## Examination **Exam Type:** [CT/MRI/X-Ray/Ultrasound/PET/Nuclear Medicine scan] **Body Part:** [

Tool: assets/radiology_report_template.md [2/2]

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Tool: assets/soap_note_template.md Description: # SOAP Note Template ## Patient Information **Patient Name:** [Last, First] or [Patient ID for teaching/research contexts] **Date of Birth:** [MM/DD/YYYY] **Medical Record Number:** [MRN] **Date of Visit:** [MM/DD/YYYY] **Time:** [HH:MM] **Location:** [Clinic, Hospital Floor, ED, etc.] **Provider:** [Your name and credentials] --- ## S - SUBJECTIVE ### Chief Complaint (CC) "[Patient's chief complaint in their own words]" ### History of Present Illn

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Tool: references/case_report_guidelines.md [1/3] Description: # Clinical Case Report Guidelines ## CARE Guidelines (CAse REport) The CARE guidelines provide a framework for transparent and complete reporting of clinical cases. The CARE checklist ensures that case reports contain all necessary information for readers to assess the validity and applicability of the findings.

Tool: references/case_report_guidelines.md [2/3] Description: Implications for clinical practice - Areas needing further investigation #### Patient Perspective (1 item) **16.

Tool: references/case_report_guidelines.md [3/3] Description: Including unnecessary details 6.

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Tool: references/clinical_trial_reporting.md [1/3] Description: # Clinical Trial Reporting Standards ## ICH-E3: Structure and Content of Clinical Study Reports The International Council for Harmonisation (ICH) E3 guideline defines the structure and content of clinical study reports (CSRs) for regulatory submission.

Tool: references/clinical_trial_reporting.md [2/3] Description: assessment - Outcome **10.2.4 Adverse Events Leading to Discontinuation** - AEs leading to study drug discontinuation - Frequency and type - Relationship to study drug **10.2.5 Deaths** - All deaths during study and follow-up - Detailed narratives for each death - Relationship to study drug - Autopsy findings (if available) **10.3 Clinical Laboratory Evaluations** - Laboratory abnormalities - Shift tables (normal to abnormal, abnorm

Tool: references/clinical_trial_reporting.md [3/3] Description: Date of report - Reporter information - Sponsor information - Study identifier (protocol number, NCT number) **2.

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Tool: references/data_presentation.md [1/3] Description: # Data Presentation in Clinical Reports ## Tables for Clinical Data ### Table Design Principles **General guidelines:** - Clear, concise title describing table contents - Column headers with units - Row labels aligned left, data aligned appropriately (numbers right, text left) - Footnotes for abbreviations, statistical notation, special cases - Consistent decimal places (typically 1-2 for percentages, 1-3 for continuous variables) - Consis

Tool: references/data_presentation.md [2/3] Description: not receive allocated intervention (n=2) Reasons: withdrew consent before treatment Reasons: withdrew consent before treatment │ │ ┌───────────┴────────────┐ ┌──────────────┴─────────────┐ │ │ │ │ Lost to follow-up (n=3) Discontinued (n=12) Lost to follow-up (n=4) Discontinued (n=11) • Adverse events (n=8) • Adverse events (n=4) • Lack of efficacy (n=2) • Lack of efficacy (n=5) • Withdrew consent (n=2) • Withdrew consent (n=2) │ │ Analyzed

Tool: references/data_presentation.md [3/3]

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Tool: references/diagnostic_reports_standards.md [1/3] Description: # Diagnostic Reports Standards ## Radiology Reporting Standards ### American College of Radiology (ACR) Guidelines The ACR provides comprehensive practice parameters for diagnostic imaging reporting to ensure quality, consistency, and communication effectiveness. #### Core Radiology Report Components **1.

Tool: references/diagnostic_reports_standards.md [2/3] Description: dimension in cm - Additional dimensions if 3D measurement relevant - Method of measurement (gross vs.

Tool: references/diagnostic_reports_standards.md [3/3] Description: Serum/Plasma: 2345-7 - Creatinine in Serum/Plasma: 2160-0 ### Critical Value Reporting **Definition:** Results that indicate life-threatening conditions requiring immediate clinical action.

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Tool: references/medical_terminology.md [1/3] Description: # Medical Terminology and Coding Standards ## Standard Nomenclature Systems ### SNOMED CT (Systematized Nomenclature of Medicine - Clinical Terms) **Purpose:** Comprehensive clinical terminology for electronic health records **Coverage:** - Clinical findings - Symptoms - Diagnoses - Procedures - Body structures - Organisms - Substances - Pharmaceutical products - Specimens **Structure:** - Concepts with unique identifiers - Descriptions

Tool: references/medical_terminology.md [2/3] Description: Unit | Mistaken for IV or 10 | Write "international unit" | | Q.D., QD, q.d., qd | Daily | Mistaken for each other | Write "daily" | | Q.O.D., QOD, q.o.d., qod | Every other day | Mistaken for QD or QID | Write "every other day" | | Trailing zero (X.0 mg) | X mg | Decimal point missed | Never write zero after decimal (write X mg) | | Lack of leading zero (.X mg) | 0.X mg | Decimal point missed | Always write zero before decimal (write 0.

Tool: references/medical_terminology.md [3/3] Description: - **Class II**: Slight limitation.

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Tool: references/patient_documentation.md [1/4] Description: # Patient Documentation Standards ## SOAP Notes SOAP (Subjective, Objective, Assessment, Plan) is the standard format for progress notes in clinical practice. ### Purpose and Use **When to use SOAP notes:** - Daily progress notes in hospital - Outpatient visit documentation - Subspecialty consultations - Follow-up visits - Documenting response to treatment **Benefits:** - Standardized structure - Organized clinical reasoning - Facilita

Tool: references/patient_documentation.md [2/4] Description: admission or initial encounter - Guide diagnosis and treatment planning - Required within 24 hours of admission (TJC requirement) ### H&P Components #### Header Information - Patient name, DOB, MRN - Date and time of examination - Admitting diagnosis - Attending physician - Service - Location (ED, floor, ICU) #### Chief Complaint (CC) **Definition:** Brief statement of why patient is seeking care **Format:** - One sentence - Use patien

Tool: references/patient_documentation.md [3/4] Description: Dullness to percussion at bilateral bases - Auscultation: Bilateral crackles halfway up lung fields, no wheezes **Abdomen:** - Inspection: Obese, no distention - Auscultation: Normoactive bowel sounds - Percussion: Tympanic - Palpation: Soft, non-tender, no masses, no hepatosplenomegaly **Extremities:** 3+ pitting edema to mid-calf bilaterally, no cyanosis or clubbing **Skin:** Warm and dry, no rashes **Neurological:** - Mental status:

Tool: references/patient_documentation.md [4/4]

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Tool: references/peer_review_standards.md [1/3] Description: # Peer Review Standards for Clinical Manuscripts ## Overview of Clinical Manuscript Peer Review ### Purpose Peer review ensures that clinical manuscripts meet standards for scientific rigor, ethical conduct, and clear communication before publication.

Tool: references/peer_review_standards.md [2/3]

Tool: references/peer_review_standards.md [3/3] Description: comments - Table/figure comments ### Tone and Language **Use:** - Professional, collegial tone - "The authors state..." not "You state..." - "This study shows..." not "Your study shows..." - Constructive criticism - Suggestions for improvement **Avoid:** - Harsh or dismissive language - Personal pronouns - Sarcasm - Vague criticism - Unreasonable demands ### Specific and Actionable Feedback **Good:** "The sample size calculation (page

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Tool: references/regulatory_compliance.md [1/3] Description: # Regulatory Compliance for Clinical Reports ## HIPAA (Health Insurance Portability and Accountability Act) ### Overview HIPAA Privacy Rule protects individually identifiable health information (Protected Health Information, PHI).

Tool: references/regulatory_compliance.md [2/3] Description: manifestations:** Must include: - Printed name of signer - Date and time of signing - Meaning of signature (e.g., review, approval, authorship) ### Closed vs.

Tool: references/regulatory_compliance.md [3/3]

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Tool: scripts/check_deidentification.py Description: #!/usr/bin/env python3 """ Check clinical reports for HIPAA identifiers that need removal.

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Tool: scripts/compliance_checker.py Description: #!/usr/bin/env python3 """ Check clinical reports for regulatory compliance (HIPAA, GCP, FDA).

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Tool: scripts/extract_clinical_data.py Description: #!/usr/bin/env python3 """ Extract structured clinical data from reports.

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Tool: scripts/format_adverse_events.py Description: #!/usr/bin/env python3 """ Format adverse event data into tables for clinical trial reports.

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Tool: scripts/generate_report_template.py Description: #!/usr/bin/env python3 """ Interactive template generator for clinical reports.

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Tool: scripts/terminology_validator.py Description: #!/usr/bin/env python3 """ Validate medical terminology and coding in clinical reports.

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Tool: scripts/validate_case_report.py Description: #!/usr/bin/env python3 """ Validate case reports against CARE (CAse REport) guidelines.

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Tool: scripts/validate_trial_report.py Description: #!/usr/bin/env python3 """ Validate clinical trial reports against ICH-E3 structure.