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: Create report file first - Initialize {disease_name}_research_report.md Research each dimension - Use all relevant tools Update report progressively - Write findings after each dimension 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:

Report Generated

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

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

Disease Identity & Classification

Ontology Identifiers | System | ID | Source |

Synonyms & Alternative Names

Disease Hierarchy

Clinical Presentation

Symptoms & Signs

Diagnostic Criteria

Genetic & Molecular Basis

Pathogenic Variants (ClinVar)

Treatment Landscape

Biological Pathways & Mechanisms

Epidemiology & Risk Factors

Literature & Research Activity

Similar Diseases & Comorbidities

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

tooluniverse-disease-research

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