ToolUniverse Disease Research

Generate a comprehensive 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. Respond in the user's language.

---

When to Use

• User asks about any disease, syndrome, or medical condition
• Needs comprehensive disease intelligence or a detailed research report
• 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 after each dimension
4. Include citations - Every fact must reference its source tool

---

10 Research Dimensions

Dim	Section	Key Tools
1	Identity & Classification	OSL_get_efo_id, ols_search/get_efo_terms, umls_search, icd_search, snomed_search
2	Clinical Presentation	OpenTargets phenotypes, HPO lookup, MedlinePlus
3	Genetic & Molecular Basis	OpenTargets targets, ClinVar variants, GWAS associations, gnomAD
4	Treatment Landscape	OpenTargets drugs, clinical trials, GtoPdb
5	Biological Pathways	Reactome pathways, HumanBase PPI, GTEx expression, HPA
6	Epidemiology & Literature	PubMed, OpenAlex, Europe PMC, Semantic Scholar
7	Similar Diseases	OpenTargets similar entities
8	Cancer-Specific (if applicable)	CIViC genes/variants/therapies
9	Pharmacology	GtoPdb targets/interactions/ligands
10	Drug Safety	OpenTargets warnings, clinical trial AEs, FAERS

See: tool_usage_details.md for complete tool calls per section.

---

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 |

### Synonyms & Alternative Names
### Disease Hierarchy

---

## 2. Clinical Presentation
### Phenotypes (HPO)
| HPO ID | Phenotype | Description | Source |

### Symptoms & Signs
### Diagnostic Criteria

---

## 3. Genetic & Molecular Basis
### Associated Genes
| Gene | Score | Ensembl ID | Evidence | Source |

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

### Pathogenic Variants (ClinVar)

---

## 4. Treatment Landscape
### Approved Drugs
| Drug | ChEMBL ID | Mechanism | Phase | Target | Source |

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

---

## 5. Biological Pathways & Mechanisms

## 6. Epidemiology & Risk Factors

## 7. Literature & Research Activity

## 8. Similar Diseases & Comorbidities

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

## 10. Drug Safety & Adverse Events

---

## References
### Tools Used
| # | Tool | Parameters | Section | Items Retrieved |

---

Citation Format

Every piece of data MUST include its source:

In tables: Add a Source column with tool name In lists: - Finding [Source: tool_name] In prose: (Source: tool_name, query: "...") References section: Complete tool usage log with parameters

---

Progressive Update Pattern

# After each dimension's research:
# 1. Read current report
# 2. Replace placeholder with formatted content
# 3. Write back immediately
# 4. Continue to next dimension

---

Final Report Quality Checklist

• All 10 sections have content (or marked "No data available")
• Every data point has a source citation
• Executive summary reflects key findings
• References section lists all tools used
• Tables properly formatted
• No placeholder text remains

---

Expected Output Scale

For a well-studied disease (e.g., Alzheimer's), the final report should include:

• 5+ ontology IDs, 10+ synonyms, disease hierarchy
• 20+ phenotypes with HPO IDs
• 50+ genes, 30+ GWAS associations, 100+ ClinVar variants
• 20+ drugs, 50+ clinical trials
• 10+ pathways, PPI network, expression data
• 100+ publications
• 15+ similar diseases
• Drug warnings and adverse events

Total: 500+ individual data points, each with source citation.

---

Reference Files

• REPORT_TEMPLATE.md - Full report markdown template and citation format guide
• RESEARCH_PROTOCOL.md - Step-by-step code procedures, progressive update pattern, quality checklist
• tool_usage_details.md - Complete tool calls for each research dimension
• TOOLS_REFERENCE.md - Complete tool documentation
• EXAMPLES.md - Sample disease research reports