disease-research

Files (4)

• SKILL.md
• tool-reference.md · references/
• run.cpython-313.pyc · scripts/__pycache__/
• run.py · scripts/

SKILL.md (first lines)

# ToolUniverse Disease Research

The agent generates a comprehensive, citation-backed disease research report by creating a markdown file and progressively updating it across 10 research dimensions.

**IMPORTANT**: The agent should always use English disease names and search terms in tool calls, even if the user writes in another language. Original-language terms should only be tried as a fallback if English returns no results. The agent responds in the user's language.

## When to Use

This skill applies when the user:
- Asks about any disease, syndrome, or medical condition
- Needs comprehensive disease intelligence
- Wants a detailed research report with citations
- Asks "what do we know about [disease]?"

## Core Workflow: Report-First Approach

The agent should **not** show the search process to the user. Instead it follows this pattern:

1. **Create report file** — Initialize `{disease_name}_research_report.md` with the full report template
2. **Research each dimension** — Query all relevant ToolUniverse tools per dimension
3. **Update report progressively** — Write findings to the file after completing each dimension
4. **Include citations** — Every fact must reference the source tool that provided it

### The 10 Research Dimensions

| # | Dimension | Key Focus |
|---|-----------|-----------|
| 1 | Disease Identity & Classification | EFO, ICD-10, UMLS, SNOMED identifiers; synonyms; disease hierarchy |
| 2 | Clinical Presentation | HPO phenotypes; symptoms and signs; diagnostic criteria |
| 3 | Genetic & Molecular Basis | Associated genes; GWAS associations; ClinVar pathogenic variants |
| 4 | Treatment Landscape | Approved drugs; clinical trials; treatment guidelines |
| 5 | Biological Pathways & Mechanisms | Reactome pathways; PPI networks; tissue expression |
| 6 | Epidemiology & Risk Factors | Prevalence; risk factors; GWAS studies |
| 7 | Literature & Research Activity | Publication trends; key papers; research institutions |
| 8 | Similar Diseases & Comorbidities | Disease similarity scores; shared genetic basis |
| 9 | Cancer-Specific Information | CIViC variants; molecular profiles; targeted therapies (if applicable) |
| 10 | Drug Safety & Adverse Events | Drug warnings; trial adverse events; FAERS data |

### Example

```
User: "Research Parkinson's disease"

Agent actions (internal, not shown to user):
1. Create "parkinsons_disease_research_report.md" with template
2. Research DIM 1 → Update Identity section
3. Research DIM 2 → Update Clinical section
4. ... continue for all 10 dimensions
5. Present final report to user
```

## Citation Requirements

Every piece of data in the report must include its source tool. The agent should use source columns in tables, `[Source: tool_name]` annotations in lists, and parenthetical `(Source: tool_name, query: ...)` references in prose. A complete tool usage log belongs in the References section at the end of the report.

## Detailed References

For the full report template, complete tool listings per dimension, implementation examples, citation format guide, and quality checklist, see [references/tool-reference.md](references/tool-reference.md).

## Additional Resources

See [TOOLS_REFERENCE.md](TOOLS_REFERENCE.md) for complete tool documentation.
See [EXAMPLES.md](EXAMPLES.md) for sample reports.

From lamm-mit/scienceclaw, Apache-2.0.

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