Skill: aipoch-ai/rare-disease-hpo-mapper (version 1.0.0)

--- name: rare-disease-hpo-mapper description: Map patient symptoms to Human Phenotype Ontology terms for gene diagnosis. license: MIT skill-author: AIPOCH --- # Rare Disease HPO Mapper Clinical phenotype standardization tool. ## When to Use - Use this skill when the task is to Map patient symptoms to Human Phenotype Ontology terms for gene diagnosis. - Use this skill for evidence insight tasks that require explicit assumptions, bounded scope, and a reproducible output format. - Use this skill when you need a documented fallback path for missing inputs, execution errors, or partial evidence. ## Key Features - Scope-focused workflow aligned to: Map patient symptoms to Human Phenotype Ontology terms for gene diagnosis. - Packaged executable path(s): `scripts/main.py`. - Reference material available in `references/` for task-specific guidance. - Structured execution path designed to keep outputs consistent and reviewable. ## Dependencies See `## Prerequisites` above for related details. - `Python`: `3.10+`. Repository baseline for current packaged skills. - `difflib`: `unspecified`. Declared in `requirements.txt`. ## Example Usage ```bash cd "20260318/scientific-skills/Evidence Insight/rare-disease-hpo-mapper" python -m py_compile scripts/main.py python scripts/main.py --help ``` Example run plan: 1. Confirm the user input, output path, and any required config values. 2. Edit the in-file `CONFIG` block or documented parameters if the script uses fixed settings. 3. Run `python scripts/main.py` with the validated inputs. 4. Review the generated output and return the final artifact with any assumptions called out. ## Implementation Details See `## Workflow` above for related details. - Execution model: validate the request, choose the packaged workflow, and produce a bounded deliverable. - Input controls: confirm the source files, scope limits, output format, and acceptance criteria before running any script. - Primary implementation surface: `scripts/main.py`. - Reference guidance: `references/` contains supporting rules, prompts, or checklists. - Parameters to clarify first: input path, output path, scope filters, thresholds, and any domain-specific constraints. - Output discipline: keep results reproducible, identify assumptions explicitly, and avoid undocumented side effects. ## Quick Check Use this command to verify that the packaged script entry point can be parsed before deeper execution. ```bash python -m py_compile scripts/main.py ``` ## Audit-Ready Commands Use these concrete commands for validation. They are intentionally self-contained and avoid placeholder paths. ```bash python -m py_compile scripts/main.py python scripts/main.py --help ``` ## Workflow 1. Confirm the user objective, required inputs, and non-negotiable constraints before doing detailed work. 2. Validate that the request matches the documented scope and stop early if the task would require unsupported assumptions. 3. Use the packaged script path or the documented reasoning path with only the inputs that are actually available. 4. Return a structured result that separates assumptions, deliverables, risks, and unresolved items. 5. If execution fails or inputs are incomplete, switch to the fallback path and state exactly what blocked full completion. ## Use Cases - Exome/genome analysis - Rare disease diagnosis - Genetic counseling - Research cohort building ## Parameters - `symptoms`: Clinical description - `age_onset`: Pediatric/adult - `inheritance_pattern`: AD/AR/XL ## Returns - HPO term suggestions - Confidence scores - Differential diagnosis genes - Literature links ## Example "Wide-set eyes" → HP:0000316 (Hypertelorism) ## Risk Assessment | Risk Indicator | Assessment | Level | |----------------|------------|-------| | Code Execution | Python/R scripts executed locally | Medium | | Network Access | No external API calls | Low | | File System Access | Read input files, write output files | Medium | | Instruction Tampering | Standard prompt guidelines | Low | | Data Exposure | Output files saved to workspace | Low | ## Security Checklist - [ ] No hardcoded credentials or API keys - [ ] No unauthorized file system access (../) - [ ] Output does not expose sensitive information - [ ] Prompt injection protections in place - [ ] Input file paths validated (no ../ traversal) - [ ] Output directory restricted to workspace - [ ] Script execution in sandboxed environment - [ ] Error messages sanitized (no stack traces exposed) - [ ] Dependencies audited ## Prerequisites ```text # Python dependencies pip install -r requirements.txt ``` ## Evaluation Criteria ### Success Metrics - [ ] Successfully executes main functionality - [ ] Output meets quality standards - [ ] Handles edge cases gracefully - [ ] Performance is acceptable ### Test Cases 1. **Basic Functionality**: Standard input → Expected output 2. **Edge Case**: Invalid input → Graceful error handling 3. **Performance**: Large dataset → Acceptable processing time ## Lifecycle Status - **Current Stage**: Draft - **Next Review Date**: 2026-03-06 - **Known Issues**: None - **Planned Improvements**: - Performance optimization - Additional feature support ## Output Requirements Every final response should make these items explicit when they are relevant: - Objective or requested deliverable - Inputs used and assumptions introduced - Workflow or decision path - Core result, recommendation, or artifact - Constraints, risks, caveats, or validation needs - Unresolved items and next-step checks ## Error Handling - If required inputs are missing, state exactly which fields are missing and request only the minimum additional information. - If the task goes outside the documented scope, stop instead of guessing or silently widening the assignment. - If `scripts/main.py` fails, report the failure point, summarize what still can be completed safely, and provide a manual fallback. - Do not fabricate files, citations, data, search results, or execution outcomes. ## Input Validation This skill accepts requests that match the documented purpose of `rare-disease-hpo-mapper` and include enough context to complete the workflow safely. Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond: > `rare-disease-hpo-mapper` only handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill. ## References - [references/audit-reference.md](references/audit-reference.md) - Supported scope, audit commands, and fallback boundaries ## Response Template Use the following fixed structure for non-trivial requests: 1. Objective 2. Inputs Received 3. Assumptions 4. Workflow 5. Deliverable 6. Risks and Limits 7. Next Checks If the request is simple, you may compress the structure, but still keep assumptions and limits explicit when they affect correctness.

path: references/audit-reference.md
content: # Audit Reference

## Scope

- Skill: `rare-disease-hpo-mapper`
- Core purpose: Map patient symptoms to Human Phenotype Ontology terms for gene diagnosis.
- Use only within the documented workflow and category boundary defined in `SKILL.md`

## Supported Audit Paths

- `python -m py_compile scripts/main.py`
- `python scripts/main.py --help`

## Fallback Boundary

If required inputs are incomplete, the skill should still return:

- the missing required inputs
- the steps that can still be completed safely
- assumptions that need confirmation before execution
- the next checks before accepting the final deliverable


path: requirements.txt
content: difflib


path: scripts/main.py
content: #!/usr/bin/env python3
"""
Rare Disease HPO Mapper
Map patient symptoms to Human Phenotype Ontology terms.
"""

import argparse
from difflib import get_close_matches


class HPOMapper:
    """Map symptoms to HPO terms."""
    
    HPO_TERMS = {
        "HP:0001250": {"name": "Seizure", "synonyms": ["seizures", "epilepsy", "fits"]},
        "HP:0001263": {"name": "Global developmental delay", "synonyms": ["developmental delay", "DD"]},
        "HP:0004322": {"name": "Short stature", "synonyms": ["short", "small stature"]},
        "HP:0001638": {"name": "Cardiomyopathy", "synonyms": ["heart muscle disease"]},
        "HP:0000518": {"name": "Cataract", "synonyms": ["lens opacity"]},
        "HP:0001251": {"name": "Ataxia", "synonyms": ["coordination problems", "unsteady gait"]}
    }
    
    def find_hpo_term(self, symptom):
        """Find HPO term for symptom."""
        symptom_lower = symptom.lower()
        
        # Direct match
        for hpo_id, data in self.HPO_TERMS.items():
            if symptom_lower == data["name"].lower():
                return hpo_id, data
            
            for synonym in data["synonyms"]:
                if symptom_lower == synonym.lower():
                    return hpo_id, data
        
        # Fuzzy match
        all_names = []
        for data in self.HPO_TERMS.values():
            all_names.append(data["name"])
            all_names.extend(data["synonyms"])
        
        matches = get_close_matches(symptom_lower, all_names, n=1, cutoff=0.6)
        if matches:
            for hpo_id, data in self.HPO_TERMS.items():
                if matches[0] == data["name"] or matches[0] in data["synonyms"]:
                    return hpo_id, data
        
        return None, None
    
    def map_symptoms(self, symptoms):
        """Map list of symptoms to HPO terms."""
        mappings = []
        
        for symptom in symptoms:
            hpo_id, data = self.find_hpo_term(symptom)
            
            if hpo_id:
                mappings.append({
                    "symptom": symptom,
                    "hpo_id": hpo_id,
                    "hpo_name": data["name"],
                    "confidence": "high"
                })
            else:
                mappings.append({
                    "symptom": symptom,
                    "hpo_id": None,
                    "hpo_name": "Unknown",
                    "confidence": "none"
                })
        
        return mappings


def main():
    parser = argparse.ArgumentParser(description="Rare Disease HPO Mapper")
    parser.add_argument("--symptoms", "-s", required=True, help="Comma-separated symptoms")
    
    args = parser.parse_args()
    
    mapper = HPOMapper()
    
    symptoms = [s.strip() for s in args.symptoms.split(",")]
    
    mappings = mapper.map_symptoms(symptoms)
    
    print(f"\n{'='*60}")
    print("HPO MAPPING RESULTS")
    print(f"{'='*60}\n")
    
    for m in mappings:
        if m["hpo_id"]:
            print(f"✓ {m['symptom']} → {m['hpo_id']} ({m['hpo_name']})")
        else:
            print(f"✗ {m['symptom']} → No match found")
    
    print(f"\n{'='*60}\n")


if __name__ == "__main__":
    main()


Security scan verdicts — ClawScan: clean | static analysis: clean | VirusTotal: clean | SkillSpector: clean (LOW)