/profile-report

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

📋 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

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

Dependencies

**Required**:

• Python 3.10+ (standard library only)

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