@pikaa-ai/pikaa 0.3.22 → 0.3.24

package/skills/clinical-reports/SKILL.md

@@ -1,248 +0,0 @@
----
-name: clinical-reports
-description: Create safety-bounded draft structures and run local deterministic checks for clinical case, diagnostic, trial, safety, and aggregate research reports. Use only with synthetic, de-identified, or aggregate inputs and verified source-fact manifests; every output requires qualified review.
-license: MIT
-compatibility: Requires Python 3.11+ only for optional dependency-free local scripts; no network access, credentials, external models, or image services.
-metadata:
-  version: "2.0"
-  skill-author: K-Dense Inc.
----
-
-# 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
-
-| Artifact | Primary route | Important boundary |
-|---|---|---|
-| Case report for publication | CARE 2013 checklist and 2017 explanation | Publication consent, privacy, journal policy, and clinical accuracy require human verification |
-| Radiology draft scaffold | ACR 2025 communication practice parameter plus modality-specific ACR material | A qualified radiologist authors findings/impression and handles nonroutine communication |
-| Pathology draft scaffold | Current specimen-specific CAP Cancer Protocol, if applicable | A qualified pathologist selects the protocol/version and authors diagnosis |
-| Laboratory draft scaffold | 42 CFR 493.1291 and laboratory policy | The performing laboratory controls results, reference intervals, corrections, and release |
-| Randomized-trial results report | CONSORT 2025 plus every applicable current extension | CONSORT is reporting guidance, not a conduct or submission standard |
-| Randomized-trial protocol report | SPIRIT 2025 plus applicable extensions | SPIRIT is for protocols, not results or CSRs |
-| Clinical Study Report | ICH E3 plus E3 Q&A; consider ICH E6(R3) and regional requirements | E3 is adaptable guidance, not a rigid universal template |
-| Pre-approval safety report | ICH E2A; E2B(R3) for electronic ICSR data; applicable regional law/guidance | Qualified sponsor/investigator safety assessment controls reportability and timing |
-| Post-approval individual safety report | ICH E2D(R1), E2B(R3), and regional requirements | Do not automate case assessment, coding, or submission |
-| Aggregate safety presentation | Protocol/SAP, ICH E3, CONSORT Harms, and applicable FDA/ICH guidance | Aggregate tables never determine individual-case reportability |
-| Aggregate research summary | Study-design-specific reporting guideline and source protocol/SAP | State population, estimand, denominator, missingness, and limitations exactly as verified |
-
-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
-
-```bash
-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:
-
-```bash
-PYTHONDONTWRITEBYTECODE=1 python3 scripts/validate_case_report.py \
-  ./case-report-draft.json
-```
-
-ICH E3, CONSORT 2025, or SPIRIT 2025 structure:
-
-```bash
-PYTHONDONTWRITEBYTECODE=1 python3 scripts/validate_trial_report.py \
-  ./trial-report-manifest.json
-```
-
-Aggregate adverse-event table:
-
-```bash
-PYTHONDONTWRITEBYTECODE=1 python3 scripts/format_adverse_events.py \
-  ./aggregate-ae.csv --metadata ./safety-aggregate.json \
-  --output ./aggregate-ae-table.md
-```
-
-Terminology schema:
-
-```bash
-PYTHONDONTWRITEBYTECODE=1 python3 scripts/terminology_validator.py \
-  ./terminology-manifest.json
-```
-
-De-identification process documentation:
-
-```bash
-PYTHONDONTWRITEBYTECODE=1 python3 scripts/check_deidentification.py \
-  ./deidentification-process.json
-```
-
-Traceability and consistency:
-
-```bash
-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;
-- CSR or regulatory safety output: sponsor regulatory and medical review;
-- publication: all accountable authors and target-journal checks.
-
-Never sign or submit on another person’s behalf.
-
-## Case Reports
-
-Use `assets/case_report_template.json` and `references/case_report_guidelines.md`.
-
-- CARE’s current core checklist remains the 2013 checklist.
-- Report only what the verified record supports.
-- Do not turn a case into clinical advice or generalize causality from one case.
-- Patient perspective and informed-consent status must be recorded accurately; do not draft a false consent statement.
-- De-identification and consent are separate controls. Consent does not erase privacy risk.
-
-## Diagnostic Report Scaffolds
-
-Use the radiology, pathology, or laboratory JSON asset and `references/diagnostic_reports_standards.md`.
-
-- The assets are field maps, not diagnostic authoring systems.
-- Never generate findings, impressions, diagnoses, grades, stages, reference intervals, critical thresholds, or follow-up recommendations.
-- Preserve preliminary/final/corrected status and source-system version.
-- Use current, exact CAP protocol and version for the specimen; do not maintain a generic cancer staging default.
-- Communication and correction actions remain with the responsible clinical service.
-
-The former SOAP, H&P, consultation, and discharge-summary interfaces were removed. Do not recreate patient-care notes, medication plans, triage instructions, billing support, or disposition advice.
-
-## Trial, CSR, and Safety Reporting
-
-Read `references/clinical_trial_reporting.md` and `references/safety_reporting.md`.
-
-- CONSORT 2025 has 30 minimum items for randomized-trial results; select relevant extensions from the current official catalogue.
-- SPIRIT 2025 has 34 minimum items for randomized-trial protocols and supersedes SPIRIT 2013.
-- ICH E3 remains the CSR basis; its 2012 Q&A explicitly permits justified adaptation.
-- ICH E6(R3) consolidated Principles, Annex 1, and Annex 2 were adopted on 16 June 2026; regional implementation can differ.
-- Distinguish seriousness from severity and an adverse event from a suspected adverse reaction.
-- ICH E2B(R3) defines electronic ICSR data/message structure; it is not an aggregate-table format or a reportability decision rule.
-- ICH E2D(R1), adopted 15 September 2025, addresses post-approval individual case safety reporting; aggregate periodic reporting is addressed separately.
-- FDA requirements and electronic submission routes are role-, product-, study-, and date-specific. This skill never files or transmits.
-
-## Privacy
-
-Read `references/privacy_and_deidentification.md`.
-
-- Handle only the minimum necessary data locally.
-- HHS recognizes Safe Harbor and Expert Determination under 45 CFR 164.514(b).
-- Safe Harbor also requires no actual knowledge that remaining information can identify an individual.
-- Expert Determination must be performed and documented by an appropriately qualified expert.
-- A checklist or pattern scan cannot establish de-identification or HIPAA compliance.
-- Rare conditions, small cells, dates, free text, images, metadata, and combinations of quasi-identifiers can retain re-identification risk.
-
-## Assets
-
-All assets contain synthetic schemas only and start blocked:
-
-- `assets/case_report_template.json`
-- `assets/radiology_report_template.json`
-- `assets/pathology_report_template.json`
-- `assets/lab_report_template.json`
-- `assets/clinical_trial_csr_template.json`
-- `assets/clinical_trial_results_template.json`
-- `assets/trial_protocol_reporting_checklist.json`
-- `assets/clinical_trial_safety_aggregate_template.json`
-- `assets/adverse_event_aggregate_input_template.csv`
-- `assets/research_summary_template.json`
-- `assets/deidentification_process_checklist.json`
-- `assets/quality_review_checklist.json`
-- `assets/provenance_manifest_template.json`
-- `assets/terminology_manifest_template.json`
-- `assets/consistency_manifest_template.json`
-
-## References
-
-- `references/README.md` — safe use and file map
-- `references/report_type_routing.md` — artifact-to-guidance routing
-- `references/case_report_guidelines.md` — CARE structure and publication safeguards
-- `references/diagnostic_reports_standards.md` — ACR, CAP, and CLIA boundaries
-- `references/clinical_trial_reporting.md` — CONSORT 2025, SPIRIT 2025, ICH E3/E6(R3)
-- `references/safety_reporting.md` — ICH E2/FDA safety distinctions
-- `references/privacy_and_deidentification.md` — HHS methods and limitations
-- `references/medical_terminology.md` — versioned terminology and schema checks
-- `references/data_presentation.md` — denominators, units, missingness, and aggregate tables
-- `references/professional_review.md` — ethics, accountability, and sign-off
-- `references/sources.md` — official source ledger, checked 2026-07-23
-
-## Final Handoff
-
-State:
-
-1. artifact type and exact guidance/version used;
-2. allowed data class and local-only handling;
-3. unresolved `null`, `missing`, conflicts, and unsupported claims;
-4. provenance and deterministic-check results;
-5. required qualified reviewers;
-6. the draft/non-submission warning.
-
-Never say “compliant,” “HIPAA-safe,” “validated clinically,” “approved,” “ready to file,” or “ready to submit.”

package/skills/clinical-reports/references/README.md

@@ -1,34 +0,0 @@
-# Clinical Reports References
-
-These references support local, deterministic drafting and review. They are not clinical, legal, regulatory, privacy, publication, or accreditation advice and do not establish compliance.
-
-## Safety boundary
-
-- Use only synthetic, de-identified, or aggregate data.
-- Populate drafts only from verified authorized source facts.
-- Do not diagnose, treat, dose, triage, interpret raw observations, fabricate results, sign, file, or submit.
-- Do not use external models, APIs, image tools, or cross-skill calls.
-- Keep every output marked as a draft requiring qualified review.
-
-## File map
-
-| File | Use |
-|---|---|
-| `report_type_routing.md` | Select the artifact and exact source family before drafting |
-| `case_report_guidelines.md` | CARE case-report structure, consent, and publication safeguards |
-| `diagnostic_reports_standards.md` | Radiology, pathology, and laboratory field boundaries |
-| `clinical_trial_reporting.md` | CONSORT 2025, SPIRIT 2025, ICH E3, and ICH E6(R3) |
-| `safety_reporting.md` | ICH E2 and FDA safety-reporting distinctions |
-| `privacy_and_deidentification.md` | HHS de-identification methods and process limits |
-| `medical_terminology.md` | Versioned terminology and syntax-versus-semantics limits |
-| `data_presentation.md` | Aggregate tables, denominators, units, dates, and missingness |
-| `professional_review.md` | Ethics, accountability, review, and sign-off |
-| `sources.md` | Dated official-source ledger |
-
-## Source handling
-
-`sources.md` records primary or official sources checked on 2026-07-23. Requirements, regional adoption, controlled terminologies, and professional standards can change. Before real-world use, a qualified reviewer must verify the current official source, applicable jurisdiction, institution, sponsor procedure, protocol, statistical analysis plan, and target-journal instructions.
-
-## Terminology
-
-“Required” in these references means required by the cited source within its stated scope, not universally required. “Complete” means structurally present in a manifest, not clinically correct. Script results never authorize use, release, signature, filing, or submission.