ToolUniverse Disease Research

Generate a comprehensive, detailed disease research report with full source citations. The report is created as a markdown file and progressively updated during research.

IMPORTANT: Always use English disease names and search terms in tool calls, even if the user writes in another language. Only try original-language terms as a fallback if English returns no results. Respond in the user's language.

When to Use

Apply 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

DO NOT show the search process to the user. Instead:

1. Create report file first - Initialize {disease_name}_research_report.md
2. Research each dimension - Use all relevant tools
3. Update report progressively - Write findings to file after each dimension
4. Include citations - Every fact must reference its source tool

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

Report Template

Create this file structure at the start:

# Disease Research Report: {Disease Name}

**Report Generated**: {date}
**Disease Identifiers**: (to be filled)

---

## Executive Summary

(Brief 3-5 sentence overview - fill after all research complete)

---

## 1. Disease Identity & Classification

### Ontology Identifiers
| System | ID | Source |
|--------|-----|--------|
| EFO | | |
| ICD-10 | | |
| UMLS CUI | | |
| SNOMED CT | | |

### Synonyms & Alternative Names
- (list with source)

### Disease Hierarchy
- Parent: 
- Subtypes:

**Sources**: (list tools used)

---

## 2. Clinical Presentation

### Phenotypes (HPO)
| HPO ID | Phenotype | Description | Source |
|--------|-----------|-------------|--------|

### Symptoms & Signs
- (list with source)

### Diagnostic Criteria
- (from literature/MedlinePlus)

**Sources**: (list tools used)

---

## 3. Genetic & Molecular Basis

### Associated Genes
| Gene | Score | Ensembl ID | Evidence | Source |
|------|-------|------------|----------|--------|

### GWAS Associations
| SNP | P-value | Odds Ratio | Study | Source |
|-----|---------|------------|-------|--------|

### Pathogenic Variants (ClinVar)
| Variant | Clinical Significance | Condition | Source |
|---------|----------------------|-----------|--------|

**Sources**: (list tools used)

---

## 4. Treatment Landscape

### Approved Drugs
| Drug | ChEMBL ID | Mechanism | Phase | Target | Source |
|------|-----------|-----------|-------|--------|--------|

### Clinical Trials
| NCT ID | Title | Phase | Status | Intervention | Source |
|--------|-------|-------|--------|--------------|--------|

### Treatment Guidelines
- (from literature)

**Sources**: (list tools used)

---

## 5. Biological Pathways & Mechanisms

### Key Pathways
| Pathway | Reactome ID | Genes Involved | Source |
|---------|-------------|----------------|--------|

### Protein-Protein Interactions
- (tissue-specific networks)

### Expression Patterns
| Tissue | Expression Level | Source |
|--------|------------------|--------|

**Sources**: (list tools used)

---

## 6. Epidemiology & Risk Factors

### Prevalence & Incidence
- (from literature)

### Risk Factors
| Factor | Evidence | Source |
|--------|----------|--------|

### GWAS Studies
| Study | Sample Size | Findings | Source |
|-------|-------------|----------|--------|

**Sources**: (list tools used)

---

## 7. Literature & Research Activity

### Publication Trends
- Total publications (5 years): 
- Current year: 
- Trend: 

### Key Publications
| PMID | Title | Year | Citations | Source |
|------|-------|------|-----------|--------|

### Research Institutions
- (from OpenAlex)

**Sources**: (list tools used)

---

## 8. Similar Diseases & Comorbidities

### Similar Diseases
| Disease | Similarity Score | Shared Genes | Source |
|---------|-----------------|--------------|--------|

### Comorbidities
- (from literature/clinical data)

**Sources**: (list tools used)

---

## 9. Cancer-Specific Information (if applicable)

### CIViC Variants
| Gene | Variant | Evidence Level | Clinical Significance | Source |
|------|---------|----------------|----------------------|--------|

### Molecular Profiles
- (biomarkers)

### Targeted Therapies
| Therapy | Target | Evidence | Source |
|---------|--------|----------|--------|

**Sources**: (list tools used)

---

## 10. Drug Safety & Adverse Events

### Drug Warnings
| Drug | Warning Type | Description | Source |
|------|--------------|-------------|--------|

### Clinical Trial Adverse Events
| Trial | Drug | Adverse Event | Frequency | Source |
|-------|------|---------------|-----------|--------|

### FAERS Reports
- (FDA adverse event data)

**Sources**: (list tools used)

---

## References

### Data Sources Used
| Tool | Query | Section |
|------|-------|---------|

### Database Versions
- OpenTargets: (version/date)
- ClinVar: (version/date)
- GWAS Catalog: (version/date)