Clinical Reports

Clinical Reports

Purpose

Prepare draft reporting structures, aggregate tables, and review manifests from verified authorized facts. Route each artifact to the correct reporting guidance, preserve provenance, and stop when source support or qualified review is missing.

This skill does not establish legal, regulatory, ethical, journal, accreditation, or institutional compliance. Its scripts check structure and internal consistency only.

Non-Negotiable Boundary

Never:

• diagnose, recommend treatment, choose or change dosing, triage, or provide return precautions;
• interpret images, specimens, raw laboratory results, symptoms, or other clinical observations;
• invent, infer, normalize, “complete,” or silently reconcile observations, results, dates, units, denominators, causality, expectedness, seriousness, outcomes, or conclusions;
• create an individual case safety report from patient-level narrative or decide reportability;
• sign, attest, approve, file, transmit, submit, amend a source record, or act as a licensed clinician, pathologist, radiologist, laboratorian, safety physician, statistician, privacy officer, attorney, or regulatory professional;
• use real PHI in examples, assets, tests, prompts, logs, or external services;
• call an external LLM, image service, API, or another skill.

All generated artifacts must remain visibly marked:

DRAFT — NOT FOR CLINICAL USE, SIGNATURE, FILING, OR SUBMISSION. Populate only from verified authorized source records. Qualified review and sign-off are required.

If the request crosses a boundary, stop the unsafe portion. Offer a blank structured template, a source-fact manifest, or a deterministic structural check. Direct clinical or regulatory decisions to the responsible qualified professional.

Input Gate

Proceed only when all conditions are true:

1. Purpose is explicit: publication draft, diagnostic-report scaffold, trial-results manuscript, protocol reporting review, CSR draft, aggregate safety table, or aggregate research summary.
2. Data class is allowed: synthetic, deidentified, or aggregate.
3. Authority is documented: the requester is authorized to use the records for the stated purpose.
4. Local-only handling is feasible: no upload, remote API, telemetry, or credential is needed.
5. Minimum necessary is defined: exclude fields not needed for the artifact.
6. Provenance exists: every populated field or claim maps to one or more verified source-fact IDs.
7. Review owner is identified: qualified clinical, statistical, safety, privacy, legal, journal, and/or regulatory review as applicable.

Do not accept raw free-text patient records when a structured source-fact manifest can be supplied. Do not copy direct identifiers into this skill’s templates or scripts.

Route Before Drafting

Read references/report_type_routing.md before choosing a route. Use the dated primary-source ledger in references/sources.md; check the live official source when requirements could have changed.

Safe Drafting Workflow

1. Create a source-fact manifest

Use assets/provenance_manifest_template.json. Record only local record locators, field paths, verification state, verifier role, verification date, and a SHA-256 value hash. Do not duplicate source content or direct identifiers.

Every draft claim or populated field must cite one or more fact IDs. Unsupported content remains null or missing; never replace it with plausible text.

2. Generate the correct template

PYTHONDONTWRITEBYTECODE=1 python3 scripts/generate_report_template.py --list
PYTHONDONTWRITEBYTECODE=1 python3 scripts/generate_report_template.py \
  --type case-report \
  --output ./case-report-draft.json

The generator copies a fail-closed JSON template. It does not populate clinical content, create directories, overwrite files by default, or certify readiness.

3. Populate verified fields only

• Keep draft_status unchanged.
• Replace null only when a verified fact ID supports the field.
• Preserve uncertainty and “not assessed” exactly as recorded.
• Do not translate a raw observation into a diagnosis, code, grade, stage, seriousness, causality, expectedness, or recommendation.
• Use not_applicable_with_rationale only when a qualified reviewer supplied the rationale.
• Keep source record and draft separate.

4. Run deterministic checks

CARE structure:

PYTHONDONTWRITEBYTECODE=1 python3 scripts/validate_case_report.py \
  ./case-report-draft.json

ICH E3, CONSORT 2025, or SPIRIT 2025 structure:

PYTHONDONTWRITEBYTECODE=1 python3 scripts/validate_trial_report.py \
  ./trial-report-manifest.json

Aggregate adverse-event table:

PYTHONDONTWRITEBYTECODE=1 python3 scripts/format_adverse_events.py \
  ./aggregate-ae.csv --metadata ./safety-aggregate.json \
  --output ./aggregate-ae-table.md

Terminology schema:

PYTHONDONTWRITEBYTECODE=1 python3 scripts/terminology_validator.py \
  ./terminology-manifest.json

De-identification process documentation:

PYTHONDONTWRITEBYTECODE=1 python3 scripts/check_deidentification.py \
  ./deidentification-process.json

Traceability and consistency:

PYTHONDONTWRITEBYTECODE=1 python3 scripts/provenance_validator.py ./provenance.json
PYTHONDONTWRITEBYTECODE=1 python3 scripts/consistency_checker.py ./consistency.json

These tools use the Python standard library, local bounded files, and no network, dynamic evaluation, serialization code execution, or patient-record extraction. A successful result still says review is required.

5. Apply the right review

At minimum:

• clinical facts and interpretations: qualified clinician for the specialty;
• statistical results, populations, estimands, denominators, and missingness: qualified statistician;
• safety coding, seriousness, causality, expectedness, and reportability: qualified safety professional;
• HIPAA, consent, authorization, and disclosure: privacy/legal/institutional review;