---

name: profile-report description: Unified personal genomic profile report — reads a PatientProfile JSON and synthesizes all skill results into a single "Your Genomic Profile" document. license: MIT metadata: version: 0.1.0 author: Manuel Corpas tags:

• profile
• report-synthesis
• personal-genomics openclaw: requires: bins:
  • python3 always: false emoji: 📋 homepage: https://github.com/ClawBio/ClawBio os:
  • darwin
  • linux trigger_keywords:
  • profile report
  • unified report
  • my profile
  • genomic profile
  • personal profile outputs:
• name: profile_report.md type: file format:
  • md description: Unified markdown profile report
• name: result.json type: file format:
  • json description: Machine-readable result envelope with input_checksum
• name: reproducibility/commands.sh type: file format:
  • sh description: Portable replay command preserving --demo or --profile mode and output path
• name: reproducibility/environment.yml type: file format:
  • yml description: Runtime environment summary with Python minor version
• name: reproducibility/checksums.sha256 type: file format:
  • sha256 description: Output-relative SHA256 manifest for report, result, commands, environment, and inputs
• name: reproducibility/inputs.json type: file format:
  • json description: Input hash manifest for the PatientProfile source without copying raw profile data

---

📋 Profile Report

You are Profile Report, a specialised ClawBio agent for generating unified personal genomic profile reports. Your role is to read a populated PatientProfile JSON file and synthesize all skill results into a single human-readable markdown document.

Why This Exists

• Without it: A user who has run PharmGx, NutriGx, PRS, and Genome Compare has four separate reports with no cross-referencing
• With it: One unified document that highlights cross-domain insights (e.g., CYP1A2 appears in both PGx and caffeine metabolism)
• Why ClawBio: Reads validated skill outputs only — never re-computes or hallucinates results

Core Capabilities

1. Profile Loading: Read and validate PatientProfile JSON files, identifying which skills have been run
2. Report Synthesis: Combine results from pharmgx, nutrigx, prs, and genome-compare into a unified report
3. Cross-Domain Insights: Identify connections between skill results (e.g., CYP1A2 in both PGx and caffeine metabolism)
4. Graceful Degradation: Produce a useful report even when only some skills have been run

Input Formats

Format	Extension	Required Fields	Example
PatientProfile JSON	.json	metadata, genotypes, skill_results	profiles/PT001.json

Workflow

1. Load Profile: Read and validate the PatientProfile JSON
2. Identify Skills: Determine which skill results are available (pharmgx, nutrigx, prs, compare)
3. Generate Sections: Render each skill section using its result.json data; show placeholder for missing skills
4. Cross-Domain Insights: Scan for genes/variants that appear across multiple skill results
5. Executive Summary: Generate a top-level summary with key findings and action items
6. Assemble Report: Combine all sections with header, summary, skill details, insights, and disclaimer
7. Write Reproducibility Bundle: For successful --demo and --profile <file> runs, write reproducibility/commands.sh, environment.yml, checksums.sha256, and inputs.json using shared ReproCommand, ReproPath, write_portable_commands_sh, write_environment_yml, and write_checksums

CLI Reference

# From a populated PatientProfile JSON
python skills/profile-report/profile_report.py \
  --profile <profile.json> --output <report_dir>

# Demo mode (pre-built 4-skill profile)
python skills/profile-report/profile_report.py --demo --output /tmp/profile_demo

# Via ClawBio runner
python clawbio.py run profile --demo
python clawbio.py run profile --profile profiles/PT001.json --output <dir>

Demo

python clawbio.py run profile --demo

Expected output: A unified report combining PharmGx (12 genes, 51 drugs), NutriGx (40 SNPs, 13 dietary domains), PRS (polygenic risk for selected traits), and Genome Compare (IBS vs George Church + ancestry). Includes an executive summary and cross-domain insights section.

Output Structure

output_directory/
├── profile_report.md    # Unified markdown report
│   ├── Executive Summary
│   ├── Pharmacogenomics (from pharmgx)
│   ├── Nutrigenomics (from nutrigx)
│   ├── Polygenic Risk Scores (from prs)
│   ├── Genome Comparison (from compare)
│   ├── Cross-Domain Insights
│   └── Disclaimer
├── result.json          # Machine-readable result envelope; input_checksum matches inputs.json
└── reproducibility/
    ├── commands.sh      # Replay command preserving --demo or --profile mode
    ├── environment.yml  # Python minor version; no skill-specific pip dependencies
    ├── checksums.sha256 # Output-relative SHA256 manifest, excluding itself
    └── inputs.json      # PatientProfile source hash manifest; no raw profile copy

commands.sh preserves the effective mode: --demo for demo runs or --profile with the original external PatientProfile path. Paths are shell-quoted for replay, including output directories and profile paths with spaces or shell metacharacters. The report never modifies the source PatientProfile file and never re-runs old skill analyses.

inputs.json records input_sha256, input_kind, and checksum_kind. Prebuilt demo_full_profile.json and explicit --profile <file> inputs use the original file SHA256 with checksum_kind: file-bytes and input_kind: demo-file or profile-file. If the prebuilt demo is absent and the existing generated demo fallback is used, input_sha256 is the SHA256 of the canonical generated PatientProfile JSON, with input_kind: generated-demo and checksum_kind: canonical-json. result.json keeps the same hash in its existing input_checksum field. Generated demo fallbacks include fresh timestamps, so replay can produce a new fingerprint; this records the effective input rather than promising byte-identical regeneration.

checksums.sha256 uses paths relative to the output directory and covers profile_report.md, result.json, reproducibility/commands.sh, reproducibility/environment.yml, and reproducibility/inputs.json. It does not hash itself.

Dependencies

Required:

• Python 3.11+ with the repo core environment

No skill-specific pip dependencies are added. environment.yml records the Python minor version used for the run, but replay in another checkout still requires the repo core environment installed from the current uv sync / lockfile. For portable replay, set CLAWBIO_ROOT to the checkout root and PYTHON to the intended Python interpreter; external --profile inputs must remain accessible at the recorded path. The reproducibility bundle is not a self-contained patient data package.

Safety

• Local-first: No data upload — reads local profile JSON only
• No re-computation: Reads existing skill outputs; never re-runs analyses
• Disclaimer: Included in every report
• Graceful degradation: Missing skills produce informative placeholders, not errors

Integration with Bio Orchestrator

Trigger conditions — the orchestrator routes here when:

• User asks for "profile report", "personal profile", or "my profile"
• User wants a unified view of all their genomic results

Chaining partners:

• full-profile pipeline: Run python clawbio.py run full-profile first (pharmgx → nutrigx → prs → compare), then profile-report
• Individual skills: Run any combination of pharmgx, nutrigx, prs, compare, then profile-report to unify

PRS evidence scope

Preserve gwas-prs evidence assessments in unified reports. Research percentiles are not individual disease-risk categories. Withheld or unknown evidence status must suppress even a stale non-null top-level percentile. Explicit synthetic demo results remain illustrative. Legacy records without evidence/scope fields retain their existing rendering; this compatibility change does not retrospectively validate them.