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README.md

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ToolUniverse Disease Research Skill

Generate comprehensive, detailed disease research reports with full source citations using 100+ ToolUniverse tools.

Key Principles

  1. Report-First: Create a markdown file first, then populate it during research
  2. Progressive Updates: Update the report file after each research dimension
  3. Full Citations: Every data point references its source tool
  4. Comprehensive: Use ALL relevant tools, not just a subset
  5. No Process Display: Don't show the search process, just deliver the report

Workflow

User: "Research Parkinson's disease"

Agent (internal actions - NOT shown to user):
1. Create "parkinsons_disease_research_report.md"
2. Research each of 10 dimensions
3. Update report file after each dimension
4. Track all tool usage for references

Agent (to user):
→ Presents final comprehensive report

Report Structure (10 Sections)

# Section Tools Used Content
1 Identity & Classification OSL, OLS, UMLS, ICD, SNOMED IDs, synonyms, hierarchy
2 Clinical Presentation OpenTargets, HPO, MedlinePlus Phenotypes, symptoms
3 Genetic Basis OpenTargets, ClinVar, GWAS Genes, variants, associations
4 Treatment Landscape OpenTargets, ClinicalTrials, GtoPdb Drugs, trials, pipeline
5 Pathways & Mechanisms Reactome, HumanBase, GTEx, HPA Pathways, PPI, expression
6 Literature PubMed, OpenAlex, Europe PMC Publications, trends
7 Similar Diseases OpenTargets Related conditions
8 Cancer-Specific CIViC Variants, evidence (if cancer)
9 Pharmacology GtoPdb Targets, interactions
10 Drug Safety OpenTargets, FAERS Warnings, adverse events

Citation Format

Every data point includes its source:

| Gene | Score | Source |
|------|-------|--------|
| APOE | 0.92 | OpenTargets_get_associated_targets_by_disease_efoId |

Report Size

A comprehensive disease report should include:

  • 500+ individual data points
  • All 10 sections populated
  • Complete references section
  • 2000+ lines for major diseases

Files

File Purpose
SKILL.md Complete protocol with tool usage
TOOLS_REFERENCE.md Tool documentation and examples
EXAMPLES.md Sample report outputs
README.md This overview

When to Use

  • User asks about any disease/syndrome
  • Need comprehensive disease intelligence
  • Want detailed report with citations
  • Researching disease mechanisms, genetics, or treatments