Multi-Omics Disease Characterization Pipeline

Characterize diseases across multiple molecular layers (genomics, transcriptomics, proteomics, pathways) to provide systems-level understanding of disease mechanisms, identify therapeutic opportunities, and discover biomarker candidates.

KEY PRINCIPLES:

1. Report-first approach - Create report file FIRST, then populate progressively
2. Disease disambiguation FIRST - Resolve all identifiers before omics analysis
3. Layer-by-layer analysis - Systematically cover all omics layers
4. Cross-layer integration - Identify genes/targets appearing in multiple layers
5. Evidence grading - Grade all evidence as T1 (human/clinical) to T4 (computational)
6. Tissue context - Emphasize disease-relevant tissues/organs
7. Quantitative scoring - Multi-Omics Confidence Score (0-100)
8. Druggable focus - Prioritize targets with therapeutic potential
9. Biomarker identification - Highlight diagnostic/prognostic markers
10. Mechanistic synthesis - Generate testable hypotheses
11. Source references - Every statement must cite tool/database
12. Completeness checklist - Mandatory section showing analysis coverage
13. English-first queries - Always use English terms in tool calls. Respond in user's language