@bgicli/bgicli 2.1.1 → 2.2.0

package/data/skills/tooluniverse-multiomic-disease-characterization/SKILL.md

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+---
+name: tooluniverse-multiomic-disease-characterization
+description: Comprehensive multi-omics disease characterization integrating genomics, transcriptomics, proteomics, pathway, and therapeutic layers for systems-level understanding. Produces a detailed multi-omics report with quantitative confidence scoring (0-100), cross-layer gene concordance analysis, biomarker candidates, therapeutic opportunities, and mechanistic hypotheses. Uses 80+ ToolUniverse tools across 8 analysis layers. Use when users ask about disease mechanisms, multi-omics analysis, systems biology of disease, biomarker discovery, or therapeutic target identification from a disease perspective.
+---
+
+# 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
+
+---
+
+## When to Use This Skill
+
+Apply when users:
+- Ask about disease mechanisms across omics layers
+- Need multi-omics characterization of a disease
+- Want to understand disease at the systems biology level
+- Ask "What pathways/genes/proteins are involved in [disease]?"
+- Need biomarker discovery for a disease
+- Want to identify druggable targets from disease profiling
+- Ask for integrated genomics + transcriptomics + proteomics analysis
+- Need cross-layer concordance analysis
+- Ask about disease network biology / hub genes
+
+**NOT for** (use other skills instead):
+- Single gene/target validation -> Use `tooluniverse-drug-target-validation`
+- Drug safety profiling -> Use `tooluniverse-adverse-event-detection`
+- General disease overview -> Use `tooluniverse-disease-research`
+- Variant interpretation -> Use `tooluniverse-variant-interpretation`
+- GWAS-specific analysis -> Use `tooluniverse-gwas-*` skills
+- Pathway-only analysis -> Use `tooluniverse-systems-biology`
+
+---
+
+## Input Parameters
+
+| Parameter | Required | Description | Example |
+|-----------|----------|-------------|---------|
+| **disease** | Yes | Disease name, OMIM ID, EFO ID, or MONDO ID | `Alzheimer disease`, `MONDO_0004975` |
+| **tissue** | No | Tissue/organ of interest | `brain`, `liver`, `blood` |
+| **focus_layers** | No | Specific omics layers to emphasize | `genomics`, `transcriptomics`, `pathways` |
+
+---
+
+## Multi-Omics Confidence Score (0-100)
+
+### Score Components
+
+**Data Availability (0-40 points)**:
+- Genomics data available (GWAS or rare variants): 10 points
+- Transcriptomics data available (DEGs or expression): 10 points
+- Protein data available (PPI or expression): 5 points
+- Pathway data available (enriched pathways): 10 points
+- Clinical/drug data available (approved drugs or trials): 5 points
+
+**Evidence Concordance (0-40 points)**:
+- Multi-layer genes (appear in 3+ layers): up to 20 points (2 per gene, max 10 genes)
+- Consistent direction (genetics + expression concordant): 10 points
+- Pathway-gene concordance (genes found in enriched pathways): 10 points
+
+**Evidence Quality (0-20 points)**:
+- Strong genetic evidence (GWAS p < 5e-8): 10 points
+- Clinical validation (approved drugs): 10 points
+
+### Score Interpretation
+
+| Score | Tier | Interpretation |
+|-------|------|----------------|
+| **80-100** | Excellent | Comprehensive multi-omics coverage, high confidence, strong cross-layer concordance |
+| **60-79** | Good | Good coverage across most layers, some gaps |
+| **40-59** | Moderate | Moderate coverage, limited cross-layer integration |
+| **0-39** | Limited | Limited data, single-layer analysis dominates |
+
+### Evidence Grading System
+
+| Tier | Symbol | Criteria | Examples |
+|------|--------|----------|----------|
+| **T1** | [T1] | Direct human evidence, clinical proof | FDA-approved drug, GWAS hit (p<5e-8), clinical trial result |
+| **T2** | [T2] | Experimental evidence | Differential expression (validated), functional screen, mouse KO |
+| **T3** | [T3] | Computational/database evidence | PPI network, pathway mapping, expression correlation |
+| **T4** | [T4] | Annotation/prediction only | GO annotation, text-mined association, predicted interaction |
+
+---
+
+## Report Template
+
+Create this file structure at the start: `{disease_name}_multiomic_report.md`
+
+```markdown
+# Multi-Omics Disease Characterization: {Disease Name}
+
+**Report Generated**: {date}
+**Disease Identifiers**: (to be filled)
+**Multi-Omics Confidence Score**: (to be calculated)
+
+---
+
+## Executive Summary
+
+(2-3 sentence disease mechanism synthesis - fill after all layers complete)
+
+---
+
+## 1. Disease Definition & Context
+
+### Disease Identifiers
+| System | ID | Source |
+|--------|-----|--------|
+
+### Description
+### Synonyms
+### Disease Hierarchy (parents/children)
+### Affected Tissues/Organs
+### Therapeutic Areas
+
+**Sources**: (tools used)
+
+---
+
+## 2. Genomics Layer
+
+### 2.1 GWAS Associations
+| SNP | P-value | Effect | Gene | Study | Source |
+|-----|---------|--------|------|-------|--------|
+
+### 2.2 GWAS Studies Summary
+| Study ID | Trait | Sample Size | Year | Source |
+|----------|-------|-------------|------|--------|
+
+### 2.3 Associated Genes (Genetic Evidence)
+| Gene | Ensembl ID | Association Score | Evidence Type | Source |
+|------|------------|-------------------|---------------|--------|
+
+### 2.4 Rare Variants (ClinVar)
+| Variant | Gene | Clinical Significance | Source |
+|---------|------|-----------------------|--------|
+
+### Genomics Layer Summary
+- Total GWAS hits:
+- Top genes by genetic evidence:
+- Genetic architecture:
+
+**Sources**: (tools used)
+
+---
+
+## 3. Transcriptomics Layer
+
+### 3.1 Differential Expression Studies
+| Experiment | Condition | Up-regulated | Down-regulated | Source |
+|------------|-----------|--------------|----------------|--------|
+
+### 3.2 Expression Atlas Disease Evidence
+| Gene | Score | Source |
+|------|-------|--------|
+
+### 3.3 Tissue Expression Patterns (GTEx/HPA)
+| Gene | Tissue | Expression Level | Source |
+|------|--------|-----------------|--------|
+
+### 3.4 Biomarker Candidates (Expression-Based)
+| Gene | Tissue Specificity | Fold Change | Evidence | Source |
+|------|-------------------|-------------|----------|--------|
+
+### Transcriptomics Layer Summary
+- Differential expression datasets:
+- Top DEGs:
+- Tissue-specific patterns:
+
+**Sources**: (tools used)
+
+---
+
+## 4. Proteomics & Interaction Layer
+
+### 4.1 Protein-Protein Interactions (STRING)
+| Protein A | Protein B | Score | Source |
+|-----------|-----------|-------|--------|
+
+### 4.2 Hub Genes (Network Centrality)
+| Gene | Degree | Betweenness | Role | Source |
+|------|--------|-------------|------|--------|
+
+### 4.3 Protein Complexes (IntAct)
+| Complex | Members | Function | Source |
+|---------|---------|----------|--------|
+
+### 4.4 Tissue-Specific PPI Network
+| Gene | Interaction Score | Tissue | Source |
+|------|-------------------|--------|--------|
+
+### Proteomics Layer Summary
+- Total PPIs:
+- Hub genes:
+- Network modules:
+
+**Sources**: (tools used)
+
+---
+
+## 5. Pathway & Network Layer
+
+### 5.1 Enriched Pathways (Enrichr/Reactome)
+| Pathway | Database | P-value | Genes | Source |
+|---------|----------|---------|-------|--------|
+
+### 5.2 Reactome Pathway Details
+| Pathway ID | Name | Genes Involved | Source |
+|------------|------|----------------|--------|
+
+### 5.3 KEGG Pathways
+| Pathway ID | Name | Description | Source |
+|------------|------|-------------|--------|
+
+### 5.4 WikiPathways
+| Pathway ID | Name | Organism | Source |
+|------------|------|----------|--------|
+
+### Pathway Layer Summary
+- Top enriched pathways:
+- Key pathway nodes:
+- Cross-pathway connections:
+
+**Sources**: (tools used)
+
+---
+
+## 6. Gene Ontology & Functional Annotation
+
+### 6.1 Biological Processes
+| GO Term | Name | P-value | Genes | Source |
+|---------|------|---------|-------|--------|
+
+### 6.2 Molecular Functions
+| GO Term | Name | P-value | Genes | Source |
+|---------|------|---------|-------|--------|
+
+### 6.3 Cellular Components
+| GO Term | Name | P-value | Genes | Source |
+|---------|------|---------|-------|--------|
+
+**Sources**: (tools used)
+
+---
+
+## 7. Therapeutic Landscape
+
+### 7.1 Approved Drugs
+| Drug | ChEMBL ID | Mechanism | Target | Phase | Source |
+|------|-----------|-----------|--------|-------|--------|
+
+### 7.2 Druggable Targets
+| Gene | Tractability | Modality | Clinical Precedent | Source |
+|------|-------------|----------|-------------------|--------|
+
+### 7.3 Drug Repurposing Candidates
+| Drug | Original Indication | Mechanism | Target | Source |
+|------|---------------------|-----------|--------|--------|
+
+### 7.4 Clinical Trials
+| NCT ID | Title | Phase | Status | Intervention | Source |
+|--------|-------|-------|--------|--------------|--------|
+
+### Therapeutic Summary
+- Approved drugs:
+- Clinical pipeline:
+- Novel targets:
+
+**Sources**: (tools used)
+
+---
+
+## 8. Multi-Omics Integration
+
+### 8.1 Cross-Layer Gene Concordance
+| Gene | Genomics | Transcriptomics | Proteomics | Pathways | Layers | Evidence Tier |
+|------|----------|-----------------|------------|----------|--------|---------------|
+
+### 8.2 Multi-Omics Hub Genes (Top 20)
+| Rank | Gene | Layers Found | Key Evidence | Druggable | Source |
+|------|------|-------------|--------------|-----------|--------|
+
+### 8.3 Biomarker Candidates
+| Biomarker | Type | Evidence Layers | Confidence | Source |
+|-----------|------|-----------------|------------|--------|
+
+### 8.4 Mechanistic Hypotheses
+1. (Hypothesis with supporting evidence from multiple layers)
+2. ...
+
+### 8.5 Systems-Level Insights
+- Key disrupted processes:
+- Critical pathway nodes:
+- Therapeutic intervention points:
+- Testable hypotheses:
+
+---
+
+## Multi-Omics Confidence Score
+
+| Component | Points | Max | Details |
+|-----------|--------|-----|---------|
+| Genomics data | | 10 | |
+| Transcriptomics data | | 10 | |
+| Protein data | | 5 | |
+| Pathway data | | 10 | |
+| Clinical data | | 5 | |
+| Multi-layer genes | | 20 | |
+| Direction concordance | | 10 | |
+| Pathway-gene concordance | | 10 | |
+| Genetic evidence quality | | 10 | |
+| Clinical validation | | 10 | |
+| **TOTAL** | | **100** | |
+
+**Score**: XX/100 - [Tier]
+
+---
+
+## Data Availability Checklist
+
+| Omics Layer | Data Available | Tools Used | Findings |
+|-------------|---------------|------------|----------|
+| Genomics (GWAS) | Yes/No | | |
+| Genomics (Rare Variants) | Yes/No | | |
+| Transcriptomics (DEGs) | Yes/No | | |
+| Transcriptomics (Expression) | Yes/No | | |
+| Proteomics (PPI) | Yes/No | | |
+| Proteomics (Expression) | Yes/No | | |
+| Pathways (Enrichment) | Yes/No | | |
+| Pathways (KEGG/Reactome) | Yes/No | | |
+| Gene Ontology | Yes/No | | |
+| Drugs/Therapeutics | Yes/No | | |
+| Clinical Trials | Yes/No | | |
+| Literature | Yes/No | | |
+
+---
+
+## Completeness Checklist
+
+- [ ] Disease disambiguation complete (IDs resolved)
+- [ ] Genomics layer analyzed (GWAS + variants)
+- [ ] Transcriptomics layer analyzed (DEGs + expression)
+- [ ] Proteomics layer analyzed (PPI + interactions)
+- [ ] Pathway layer analyzed (enrichment + mapping)
+- [ ] Gene Ontology analyzed (BP + MF + CC)
+- [ ] Therapeutic landscape analyzed (drugs + targets + trials)
+- [ ] Cross-layer integration complete (concordance analysis)
+- [ ] Multi-Omics Confidence Score calculated
+- [ ] Biomarker candidates identified
+- [ ] Hub genes identified
+- [ ] Mechanistic hypotheses generated
+- [ ] Executive summary written
+- [ ] All sections have source citations
+
+---
+
+## References
+
+### Data Sources Used
+| # | Tool | Parameters | Section | Items Retrieved |
+|---|------|------------|---------|-----------------|
+
+### Database Versions
+- OpenTargets: (current)
+- GWAS Catalog: (current)
+- STRING: (current)
+- Reactome: (current)
+```
+
+---
+
+## Phase 0: Disease Disambiguation (ALWAYS FIRST)
+
+**Objective**: Resolve disease to standard identifiers for all downstream queries.
+
+### Tools Used
+
+**OpenTargets_get_disease_id_description_by_name** (primary):
+- **Input**: `diseaseName` (string) - Disease name
+- **Output**: `{data: {search: {hits: [{id, name, description}]}}}`
+- **Use**: Get MONDO/EFO IDs and description
+- **CRITICAL**: Disease IDs from OpenTargets use underscore format (e.g., `MONDO_0004975`), NOT colon format
+
+**OSL_get_efo_id_by_disease_name** (secondary):
+- **Input**: `disease` (string) - Disease name
+- **Output**: `{efo_id, name}`
+- **Use**: Get EFO/MONDO ID
+
+**OpenTargets_get_disease_description_by_efoId**:
+- **Input**: `efoId` (string) - Disease ID (e.g., `MONDO_0004975`)
+- **Output**: `{data: {disease: {id, name, description, dbXRefs}}}`
+- **Use**: Get full description, cross-references (OMIM, UMLS, DOID, etc.)
+
+**OpenTargets_get_disease_synonyms_by_efoId**:
+- **Input**: `efoId` (string)
+- **Output**: `{data: {disease: {id, name, synonyms: [{relation, terms}]}}}`
+
+**OpenTargets_get_disease_therapeutic_areas_by_efoId**:
+- **Input**: `efoId` (string)
+- **Output**: `{data: {disease: {id, name, therapeuticAreas: [{id, name}]}}}`
+
+**OpenTargets_get_disease_ancestors_parents_by_efoId**:
+- **Input**: `efoId` (string)
+- **Output**: `{data: {disease: {id, name, ancestors: [{id, name}]}}}`
+
+**OpenTargets_get_disease_descendants_children_by_efoId**:
+- **Input**: `efoId` (string)
+- **Output**: `{data: {disease: {id, name, descendants: [{id, name}]}}}`
+
+**OpenTargets_map_any_disease_id_to_all_other_ids**:
+- **Input**: `inputId` (string) - Any known disease ID (e.g., `OMIM:104300`, `UMLS:C0002395`)
+- **Output**: `{data: {disease: {id, name, dbXRefs: [str], ...}}}`
+- **Use**: Cross-map between OMIM, UMLS, ICD10, DOID, etc.
+
+### Workflow
+
+1. Search by disease name to get primary ID (OpenTargets)
+2. Get full description and cross-references
+3. Get synonyms for search term expansion
+4. Get therapeutic areas for context
+5. Get disease hierarchy (parents/children)
+6. If user provided OMIM/other ID, map to MONDO/EFO first
+
+### Collision-Aware Search
+
+When disease name returns multiple hits:
+- Check if user's input matches any hit exactly
+- If ambiguous, present top 3-5 options and ask user to select
+- Always prefer the most specific disease (not parent categories)
+- For cancer, prefer the specific tumor type over generic "cancer"
+
+### Key Disease IDs to Track
+
+After disambiguation, store these for all downstream queries:
+- `efo_id` - Primary ID for OpenTargets queries (e.g., `MONDO_0004975`)
+- `disease_name` - Canonical name (e.g., `Alzheimer disease`)
+- `synonyms` - For literature search expansion
+- `therapeutic_areas` - For context
+- `dbXRefs` - Cross-references (OMIM, UMLS, DOID, etc.)
+
+---
+
+## Phase 1: Genomics Layer
+
+**Objective**: Identify genetic variants, GWAS associations, and genetically implicated genes.
+
+### Tools Used
+
+**OpenTargets_get_associated_targets_by_disease_efoId** (primary):
+- **Input**: `efoId` (string) - Disease EFO/MONDO ID
+- **Output**: `{data: {disease: {id, name, associatedTargets: {count, rows: [{target: {id, approvedSymbol}, score}]}}}}`
+- **Use**: Get ALL disease-associated genes ranked by overall evidence score
+- **NOTE**: Returns top 25 by default. For comprehensive analysis, note the total `count`
+
+**OpenTargets_get_evidence_by_datasource**:
+- **Input**: `efoId` (string), `ensemblId` (string), optional `datasourceIds` (array), `size` (int, default 50)
+- **Output**: `{data: {disease: {evidences: {count, rows: [{...evidence details}]}}}}`
+- **Use**: Get specific evidence types. Key datasourceIds for genomics:
+  - `['ot_genetics_portal']` - GWAS/genetics
+  - `['gene2phenotype', 'genomics_england', 'orphanet']` - Rare variants
+  - `['eva']` - ClinVar variants
+
+**gwas_search_associations** (GWAS Catalog):
+- **Input**: `disease_trait` (string), `size` (int, default 20)
+- **Output**: `{data: [{association_id, p_value, or_per_copy_num, or_value, beta, risk_frequency, efo_traits: [{...}], ...}], metadata: {pagination: {totalElements}}}`
+- **Use**: Get genome-wide significant associations
+- **NOTE**: Use disease name (e.g., "Alzheimer"), not ID. Returns paginated results
+
+**gwas_get_studies_for_trait**:
+- **Input**: `disease_trait` (string), `size` (int)
+- **Output**: `{data: [...studies], metadata: {pagination}}`
+- **NOTE**: May return empty if trait name does not match exactly. Try synonyms
+
+**gwas_get_variants_for_trait**:
+- **Input**: `disease_trait` (string), `size` (int)
+- **Output**: `{data: [...variants], metadata: {pagination}}`
+
+**GWAS_search_associations_by_gene**:
+- **Input**: `gene_name` (string)
+- **Output**: Associations for a specific gene
+
+**OpenTargets_search_gwas_studies_by_disease**:
+- **Input**: `diseaseIds` (array of strings), `enableIndirect` (bool, default true), `size` (int, default 10)
+- **Output**: `{data: {studies: {count, rows: [{id, studyType, traitFromSource, publicationFirstAuthor, publicationDate, pubmedId, nSamples, nCases, nControls, ...}]}}}`
+- **Use**: Get GWAS studies from OpenTargets genetics portal
+
+**clinvar_search_variants**:
+- **Input**: `condition` (string) or `gene` (string), optional `max_results` (int)
+- **Output**: List of ClinVar variants with clinical significance
+- **Use**: Rare variant / monogenic disease evidence
+
+### Workflow
+
+1. Get associated genes from OpenTargets (overall scores)
+2. For top 10-15 genes, get genetic evidence specifically via `OpenTargets_get_evidence_by_datasource`
+3. Search GWAS Catalog for associations
+4. Search OpenTargets GWAS studies
+5. Search ClinVar for rare variants
+6. For top GWAS genes, check `GWAS_search_associations_by_gene`
+
+### Gene Tracking
+
+Maintain a dictionary of genes found in genomics layer:
+```python
+genomics_genes = {
+    'PSEN1': {'score': 0.87, 'evidence': 'genetic', 'ensembl_id': 'ENSG00000080815', 'layer': 'genomics'},
+    'APP': {'score': 0.82, 'evidence': 'genetic', 'ensembl_id': 'ENSG00000142192', 'layer': 'genomics'},
+    # ...
+}
+```
+
+---
+
+## Phase 2: Transcriptomics Layer
+
+**Objective**: Identify differentially expressed genes, tissue-specific expression, and expression-based biomarkers.
+
+### Tools Used
+
+**ExpressionAtlas_search_differential**:
+- **Input**: optional `gene` (string), `condition` (string), `species` (string, default 'homo sapiens')
+- **Output**: Differential expression studies and results
+- **Use**: Find studies where genes are differentially expressed in disease
+
+**ExpressionAtlas_search_experiments**:
+- **Input**: optional `gene` (string), `condition` (string), `species` (string)
+- **Output**: Expression experiments relevant to condition
+- **Use**: Find all Expression Atlas experiments for the disease
+
+**expression_atlas_disease_target_score**:
+- **Input**: `efoId` (string), `pageSize` (int, required)
+- **Output**: Genes scored by expression evidence for the disease
+- **Use**: Get expression-based disease-gene association scores
+
+**europepmc_disease_target_score**:
+- **Input**: `efoId` (string), `pageSize` (int, required)
+- **Output**: Genes scored by literature evidence for the disease
+- **Use**: Complement expression evidence with literature-mined associations
+
+**HPA_get_rna_expression_by_source** (Human Protein Atlas):
+- **Input**: `gene_name` (string), `source_type` (string: 'tissue', 'blood', 'brain'), `source_name` (string: e.g., 'brain', 'liver')
+- **Output**: `{status, data: {gene_name, source_type, source_name, expression_value, expression_level, expression_unit}}`
+- **NOTE**: ALL 3 params required. `source_type` options: 'tissue', 'blood', 'brain', 'cell_line', 'single_cell'
+
+**HPA_get_rna_expression_in_specific_tissues**:
+- **Input**: `gene_name` (string), `tissues` (array of strings)
+- **Output**: Expression across specified tissues
+
+**HPA_get_cancer_prognostics_by_gene**:
+- **Input**: `gene_name` (string)
+- **Output**: Cancer prognostic data (if cancer context)
+
+**HPA_get_subcellular_location**:
+- **Input**: `gene_name` (string)
+- **Output**: Subcellular localization data
+
+**HPA_search_genes_by_query**:
+- **Input**: `query` (string)
+- **Output**: Matching genes in HPA
+
+### Workflow
+
+1. Search Expression Atlas for differential expression studies
+2. Get expression-based disease scores
+3. Get literature-based disease scores (EuropePMC)
+4. For top 10-15 genes from genomics layer, check tissue expression via HPA
+5. Check disease-relevant tissue expression patterns
+6. For cancer: check prognostic biomarkers
+
+### Gene Tracking
+
+Add transcriptomics genes to tracking:
+```python
+transcriptomics_genes = {
+    'APOE': {'expression_score': 0.75, 'tissues': ['brain'], 'evidence': 'differential_expression', 'layer': 'transcriptomics'},
+    # ...
+}
+```
+
+---
+
+## Phase 3: Proteomics & Interaction Layer
+
+**Objective**: Map protein-protein interactions, identify hub genes, and characterize interaction networks.
+
+### Tools Used
+
+**STRING_get_interaction_partners** (primary PPI):
+- **Input**: `protein_ids` (array of strings - gene names work), `species` (int, default 9606), `confidence_score` (float, default 0.4), `limit` (int, default 20)
+- **Output**: `{status: 'success', data: [{stringId_A, stringId_B, preferredName_A, preferredName_B, ncbiTaxonId, score, nscore, fscore, pscore, ascore, escore, dscore, tscore}]}`
+- **Use**: Get interaction partners for disease genes
+- **NOTE**: `protein_ids` is an array, NOT string. Gene symbols like `['APOE']` work
+
+**STRING_get_network**:
+- **Input**: `protein_ids` (array), `species` (int), `confidence_score` (float)
+- **Output**: Network of interactions between input proteins
+- **Use**: Build disease-specific PPI network
+
+**STRING_functional_enrichment**:
+- **Input**: `protein_ids` (array), `species` (int)
+- **Output**: Functional enrichment results (GO, KEGG, etc.)
+- **Use**: Functional characterization of disease gene set
+
+**STRING_ppi_enrichment**:
+- **Input**: `protein_ids` (array), `species` (int)
+- **Output**: Statistical test for PPI enrichment (more interactions than expected)
+- **Use**: Test if disease genes form a connected module
+
+**intact_get_interactions**:
+- **Input**: `identifier` (string - UniProt ID or gene name)
+- **Output**: Molecular interaction data from IntAct
+
+**intact_search_interactions**:
+- **Input**: `query` (string), `first` (int, default 0), `max` (int, default 25)
+- **Output**: Search results for interactions
+
+**HPA_get_protein_interactions_by_gene**:
+- **Input**: `gene_name` (string)
+- **Output**: `{gene, interactions, interactor_count, interactors: [...]}`
+
+**humanbase_ppi_analysis**:
+- **Input**: `gene_list` (array), `tissue` (string), `max_node` (int), `interaction` (string), `string_mode` (bool)
+- **Output**: Tissue-specific PPI network
+- **NOTE**: ALL params required. `interaction` options: 'coexpression', 'interaction', 'coexpression_and_interaction'. `string_mode`: true/false
+
+### Workflow
+
+1. Take top 15-20 genes from genomics + transcriptomics layers
+2. Query STRING for interaction partners of each gene
+3. Build composite PPI network using STRING_get_network
+4. Test PPI enrichment (are genes more connected than random?)
+5. Get functional enrichment from STRING
+6. For disease-relevant tissue, get tissue-specific network (HumanBase)
+7. Identify hub genes (highest degree centrality)
+8. Check IntAct for experimentally validated interactions
+
+### Hub Gene Analysis
+
+Calculate network centrality metrics:
+- **Degree**: Number of interaction partners
+- **Betweenness**: Number of shortest paths through node
+- **Hub score**: Genes with degree > mean + 1 SD are hubs
+
+---
+
+## Phase 4: Pathway & Network Layer
+
+**Objective**: Identify enriched biological pathways and cross-pathway connections.
+
+### Tools Used
+
+**enrichr_gene_enrichment_analysis** (primary enrichment):
+- **Input**: `gene_list` (array of gene symbols, min 2), `libs` (array of library names)
+- **Output**: `{status: 'success', data: '{...JSON string with enrichment results...}'}`
+- **Key libraries**: `['KEGG_2021_Human']`, `['Reactome_2022']`, `['WikiPathway_2023_Human']`, `['GO_Biological_Process_2023']`, `['GO_Molecular_Function_2023']`, `['GO_Cellular_Component_2023']`
+- **NOTE**: `data` field is a JSON string, needs parsing. Contains `connected_paths` and per-library results
+- **NOTE**: `libs` is REQUIRED as array
+
+**ReactomeAnalysis_pathway_enrichment**:
+- **Input**: `identifiers` (string - space-separated gene list), optional `page_size` (int, default 20), `include_disease` (bool), `projection` (bool)
+- **Output**: `{data: {token, analysis_type, pathways_found, pathways: [{pathway_id, name, species, is_disease, is_lowest_level, entities_found, entities_total, entities_ratio, p_value, fdr, reactions_found, reactions_total}]}}`
+- **Use**: Reactome-specific pathway enrichment with statistical testing
+
+**Reactome_map_uniprot_to_pathways**:
+- **Input**: `id` (string - UniProt accession)
+- **Output**: List of Reactome pathways containing this protein
+- **Use**: Map individual proteins to pathways
+
+**Reactome_get_pathway**:
+- **Input**: `stId` (string - Reactome stable ID, e.g., 'R-HSA-73817')
+- **Output**: Pathway details
+
+**Reactome_get_pathway_reactions**:
+- **Input**: `stId` (string)
+- **Output**: Reactions within pathway
+
+**kegg_search_pathway**:
+- **Input**: `keyword` (string)
+- **Output**: Array of KEGG pathway matches
+
+**kegg_get_pathway_info**:
+- **Input**: `pathway_id` (string, e.g., 'hsa04930')
+- **Output**: Detailed pathway information
+
+**WikiPathways_search**:
+- **Input**: `query` (string), optional `organism` (string, e.g., 'Homo sapiens')
+- **Output**: Matching community-curated pathways
+
+### Workflow
+
+1. Collect all genes from genomics + transcriptomics layers (top 20-30)
+2. Run Enrichr enrichment for KEGG, Reactome, WikiPathways
+3. Run ReactomeAnalysis for more detailed Reactome enrichment with p-values
+4. Search KEGG for disease-specific pathways
+5. Search WikiPathways for disease pathways
+6. For top Reactome pathways, get detailed reactions
+7. Identify cross-pathway connections (genes in multiple pathways)
+
+---
+
+## Phase 5: Gene Ontology & Functional Annotation
+
+**Objective**: Characterize biological processes, molecular functions, and cellular components.
+
+### Tools Used
+
+**enrichr_gene_enrichment_analysis** (GO enrichment):
+- Use with `libs=['GO_Biological_Process_2023']` for BP
+- Use with `libs=['GO_Molecular_Function_2023']` for MF
+- Use with `libs=['GO_Cellular_Component_2023']` for CC
+
+**GO_get_annotations_for_gene**:
+- **Input**: `gene_id` (string - gene symbol or UniProt ID)
+- **Output**: List of GO annotations with terms, aspects, evidence codes
+
+**GO_search_terms**:
+- **Input**: `query` (string)
+- **Output**: Matching GO terms
+
+**QuickGO_annotations_by_gene**:
+- **Input**: `gene_product_id` (string - UniProt accession, e.g., 'UniProtKB:P02649'), optional `aspect` (string: 'biological_process', 'molecular_function', 'cellular_component'), `taxon_id` (int: 9606), `limit` (int: 25)
+- **Output**: GO annotations with evidence codes
+
+**OpenTargets_get_target_gene_ontology_by_ensemblID**:
+- **Input**: `ensemblId` (string)
+- **Output**: GO terms associated with target
+
+### Workflow
+
+1. Run Enrichr GO enrichment for all 3 aspects using combined gene list
+2. For top 5 genes, get detailed GO annotations from QuickGO
+3. For top genes, get OpenTargets GO terms
+4. Summarize key biological processes, molecular functions, cellular components
+
+---
+
+## Phase 6: Therapeutic Landscape
+
+**Objective**: Map approved drugs, druggable targets, repurposing opportunities, and clinical trials.
+
+### Tools Used
+
+**OpenTargets_get_associated_drugs_by_disease_efoId** (primary):
+- **Input**: `efoId` (string), `size` (int, REQUIRED - use 100)
+- **Output**: `{data: {disease: {knownDrugs: {count, rows: [{drug: {id, name, tradeNames, maximumClinicalTrialPhase, isApproved, hasBeenWithdrawn}, phase, mechanismOfAction, target: {id, approvedSymbol}, disease: {id, name}, urls: [{url, name}]}]}}}}`
+- **Use**: All drugs associated with disease (approved + investigational)
+
+**OpenTargets_get_target_tractability_by_ensemblID**:
+- **Input**: `ensemblId` (string)
+- **Output**: Tractability assessment (small molecule, antibody, PROTAC, etc.)
+
+**OpenTargets_get_associated_drugs_by_target_ensemblID**:
+- **Input**: `ensemblId` (string), `size` (int, REQUIRED)
+- **Output**: Drugs targeting this gene/protein
+
+**search_clinical_trials**:
+- **Input**: `query_term` (string, REQUIRED), optional `condition` (string), `intervention` (string), `pageSize` (int, default 10)
+- **Output**: Clinical trial results
+- **NOTE**: `query_term` is REQUIRED even if `condition` is provided
+
+**OpenTargets_get_drug_mechanisms_of_action_by_chemblId**:
+- **Input**: `chemblId` (string)
+- **Output**: Mechanism of action details
+
+### Workflow
+
+1. Get all drugs for disease from OpenTargets
+2. For top disease-associated genes, check tractability
+3. For top genes with no approved drugs, identify repurposing candidates
+4. Search clinical trials for disease
+5. For top approved drugs, get mechanism of action
+
+### Drug Tracking
+
+```python
+drug_targets = {
+    'PSEN1': {'drugs': ['Semagacestat'], 'tractability': 'small_molecule', 'clinical_phase': 3},
+    'ACHE': {'drugs': ['Donepezil', 'Galantamine'], 'tractability': 'small_molecule', 'clinical_phase': 4},
+    # ...
+}
+```
+
+---
+
+## Phase 7: Multi-Omics Integration
+
+**Objective**: Integrate findings across all layers to identify cross-layer genes, calculate concordance, and generate mechanistic hypotheses.
+
+### Cross-Layer Gene Concordance Analysis
+
+This is the core integrative step. For each gene found in the analysis:
+
+1. **Count layers**: In how many omics layers does this gene appear?
+   - Genomics (GWAS, rare variants, genetic association)
+   - Transcriptomics (DEGs, expression score)
+   - Proteomics (PPI hub, protein expression)
+   - Pathways (enriched pathway member)
+   - Therapeutics (drug target)
+
+2. **Score genes**: Genes appearing in 3+ layers are "multi-omics hub genes"
+
+3. **Direction concordance**: Do genetics and expression agree?
+   - Risk allele + upregulated = concordant gain-of-function
+   - Risk allele + downregulated = concordant loss-of-function
+   - Discordant = needs investigation
+
+### Biomarker Identification
+
+For each multi-omics hub gene, assess biomarker potential:
+- **Diagnostic**: Gene expression distinguishes disease vs healthy
+- **Prognostic**: Expression/variant predicts outcome (cancer prognostics from HPA)
+- **Predictive**: Variant/expression predicts treatment response (pharmacogenomics)
+- **Evidence level**: Number of supporting omics layers
+
+### Mechanistic Hypothesis Generation
+
+From the integrated data:
+1. Identify the most supported biological processes (GO + pathways)
+2. Map causal chain: genetic variant -> gene expression -> protein function -> pathway disruption -> disease
+3. Identify intervention points (druggable nodes in the causal chain)
+4. Generate testable hypotheses
+
+### Confidence Score Calculation
+
+Calculate the Multi-Omics Confidence Score (0-100) based on:
+- Data availability across layers
+- Cross-layer concordance
+- Evidence quality
+- Clinical validation
+
+---
+
+## Phase 8: Report Finalization
+
+### Executive Summary
+
+Write a 2-3 sentence synthesis covering:
+- Disease mechanism in systems terms
+- Key genes/pathways identified
+- Therapeutic opportunities
+
+### Final Report Quality Checklist
+
+Before presenting to user, verify:
+- [ ] All 8 sections have content (or marked as "No data available")
+- [ ] Every data point has a source citation
+- [ ] Executive summary reflects key findings
+- [ ] Multi-Omics Confidence Score calculated
+- [ ] Top 20 genes ranked by multi-omics evidence
+- [ ] Top 10 enriched pathways listed
+- [ ] Biomarker candidates identified
+- [ ] Cross-layer concordance table complete
+- [ ] Therapeutic opportunities summarized
+- [ ] Mechanistic hypotheses generated
+- [ ] Data Availability Checklist complete
+- [ ] Completeness Checklist complete
+- [ ] References section lists all tools used
+
+---
+
+## Tool Parameter Quick Reference
+
+| Tool | Key Parameters | Notes |
+|------|---------------|-------|
+| `OpenTargets_get_disease_id_description_by_name` | `diseaseName` | Primary disambiguation |
+| `OSL_get_efo_id_by_disease_name` | `disease` | Secondary disambiguation |
+| `OpenTargets_get_associated_targets_by_disease_efoId` | `efoId` | Returns top 25 genes |
+| `OpenTargets_get_evidence_by_datasource` | `efoId`, `ensemblId`, `datasourceIds[]`, `size` | Per-gene evidence |
+| `OpenTargets_search_gwas_studies_by_disease` | `diseaseIds[]`, `size` | GWAS studies |
+| `gwas_search_associations` | `disease_trait`, `size` | GWAS Catalog |
+| `clinvar_search_variants` | `condition` or `gene`, `max_results` | Rare variants |
+| `ExpressionAtlas_search_differential` | `condition`, `species` | DEGs |
+| `expression_atlas_disease_target_score` | `efoId`, `pageSize` (REQUIRED) | Expression scores |
+| `europepmc_disease_target_score` | `efoId`, `pageSize` (REQUIRED) | Literature scores |
+| `HPA_get_rna_expression_by_source` | `gene_name`, `source_type`, `source_name` (ALL REQUIRED) | Tissue expression |
+| `STRING_get_interaction_partners` | `protein_ids[]`, `species` (9606), `limit` | PPI partners |
+| `STRING_get_network` | `protein_ids[]`, `species` | PPI network |
+| `STRING_functional_enrichment` | `protein_ids[]`, `species` | Functional enrichment |
+| `STRING_ppi_enrichment` | `protein_ids[]`, `species` | Network significance |
+| `intact_search_interactions` | `query`, `max` | Experimental PPIs |
+| `humanbase_ppi_analysis` | `gene_list[]`, `tissue`, `max_node`, `interaction`, `string_mode` (ALL REQ) | Tissue PPI |
+| `enrichr_gene_enrichment_analysis` | `gene_list[]`, `libs[]` (BOTH REQUIRED) | Pathway/GO enrichment |
+| `ReactomeAnalysis_pathway_enrichment` | `identifiers` (space-sep string) | Reactome enrichment |
+| `Reactome_map_uniprot_to_pathways` | `id` (UniProt accession) | Protein-pathway mapping |
+| `kegg_search_pathway` | `keyword` | KEGG pathway search |
+| `WikiPathways_search` | `query`, `organism` | WikiPathways search |
+| `GO_get_annotations_for_gene` | `gene_id` | GO annotations |
+| `QuickGO_annotations_by_gene` | `gene_product_id` (e.g., 'UniProtKB:P02649') | Detailed GO |
+| `OpenTargets_get_associated_drugs_by_disease_efoId` | `efoId`, `size` (REQUIRED) | Disease drugs |
+| `OpenTargets_get_target_tractability_by_ensemblID` | `ensemblId` | Druggability |
+| `search_clinical_trials` | `query_term` (REQUIRED), `condition`, `pageSize` | Clinical trials |
+| `PubMed_search_articles` | `query`, `limit` | Literature |
+| `ensembl_lookup_gene` | `gene_id`, `species` ('homo_sapiens' REQUIRED) | Gene lookup |
+| `MyGene_query_genes` | `query`, `species`, `fields`, `size` | Gene info |
+| `OpenTargets_get_similar_entities_by_disease_efoId` | `efoId`, `threshold`, `size` (ALL REQUIRED) | Similar diseases |
+
+---
+
+## Response Format Notes (Verified)
+
+### OpenTargets Associated Targets
+```json
+{
+  "data": {
+    "disease": {
+      "id": "MONDO_0004975",
+      "name": "Alzheimer disease",
+      "associatedTargets": {
+        "count": 2456,
+        "rows": [
+          {
+            "target": {"id": "ENSG00000080815", "approvedSymbol": "PSEN1"},
+            "score": 0.87
+          }
+        ]
+      }
+    }
+  }
+}
+```
+
+### GWAS Catalog Associations
+```json
+{
+  "data": [
+    {
+      "association_id": 216440893,
+      "p_value": 2e-09,
+      "or_per_copy_num": 0.94,
+      "or_value": "0.94",
+      "efo_traits": [{"..."}],
+      "risk_frequency": "NR"
+    }
+  ],
+  "metadata": {"pagination": {"totalElements": 1061816}}
+}
+```
+
+### STRING Interactions
+```json
+{
+  "status": "success",
+  "data": [
+    {
+      "stringId_A": "9606.ENSP00000252486",
+      "stringId_B": "9606.ENSP00000466775",
+      "preferredName_A": "APOE",
+      "preferredName_B": "APOC2",
+      "score": 0.999
+    }
+  ]
+}
+```
+
+### Reactome Enrichment
+```json
+{
+  "data": {
+    "token": "...",
+    "pathways_found": 154,
+    "pathways": [
+      {
+        "pathway_id": "R-HSA-1251985",
+        "name": "Nuclear signaling by ERBB4",
+        "species": "Homo sapiens",
+        "is_disease": false,
+        "is_lowest_level": true,
+        "entities_found": 3,
+        "entities_total": 47,
+        "entities_ratio": 0.00291,
+        "p_value": 4.0e-06,
+        "fdr": 0.00068,
+        "reactions_found": 3,
+        "reactions_total": 34
+      }
+    ]
+  }
+}
+```
+
+### HPA RNA Expression
+```json
+{
+  "status": "success",
+  "data": {
+    "gene_name": "APOE",
+    "source_type": "tissue",
+    "source_name": "brain",
+    "expression_value": "2714.9",
+    "expression_level": "very high",
+    "expression_unit": "nTPM"
+  }
+}
+```
+
+### Enrichr Results
+```json
+{
+  "status": "success",
+  "data": "{\"connected_paths\": {\"Path: ...\": \"Total Weight: ...\"}}"
+}
+```
+**NOTE**: The `data` field is a JSON string that needs parsing.
+
+---
+
+## Common Use Patterns
+
+### 1. Comprehensive Disease Profiling
+```
+User: "Characterize Alzheimer's disease across omics layers"
+-> Run all 8 phases
+-> Produce full multi-omics report
+```
+
+### 2. Therapeutic Target Discovery
+```
+User: "What are druggable targets for rheumatoid arthritis?"
+-> Emphasize Phase 1 (genomics), Phase 6 (therapeutics), Phase 7 (integration)
+-> Focus on tractability and clinical precedent
+```
+
+### 3. Biomarker Identification
+```
+User: "Find diagnostic biomarkers for pancreatic cancer"
+-> Emphasize Phase 2 (transcriptomics), Phase 3 (proteomics), Phase 7 (biomarkers)
+-> Focus on tissue-specific expression and diagnostic potential
+```
+
+### 4. Mechanism Elucidation
+```
+User: "What pathways are dysregulated in Crohn's disease?"
+-> Emphasize Phase 4 (pathways), Phase 5 (GO), Phase 7 (mechanistic hypotheses)
+-> Focus on pathway enrichment and cross-pathway connections
+```
+
+### 5. Drug Repurposing
+```
+User: "What existing drugs could be repurposed for ALS?"
+-> Emphasize Phase 1 (genetics), Phase 6 (therapeutic landscape), Phase 7 (repurposing)
+-> Focus on drugs targeting disease-associated genes
+```
+
+### 6. Systems Biology
+```
+User: "What are the hub genes and key pathways in type 2 diabetes?"
+-> Emphasize Phase 3 (PPI network), Phase 4 (pathways), Phase 7 (network analysis)
+-> Focus on hub genes and network modules
+```
+
+---
+
+## Edge Case Handling
+
+### Rare Diseases (limited data)
+- Genomics layer may dominate (single gene)
+- Limited GWAS data (monogenic)
+- Focus on ClinVar variants, pathway consequences
+- Confidence score will be lower (less cross-layer data)
+
+### Common Diseases (overwhelming data)
+- Thousands of GWAS associations
+- Prioritize by effect size and significance
+- Focus on top 20-30 genes for downstream analysis
+- Use strict significance thresholds (p < 5e-8)
+
+### Cancer
+- Include somatic mutations (if CIViC/cBioPortal available)
+- Check cancer prognostics via HPA
+- Include tumor-specific expression patterns
+- Clinical trial landscape may be extensive
+
+### Monogenic Diseases
+- Single gene dominates
+- ClinVar/OMIM evidence is primary
+- Pathway analysis reveals downstream effects
+- Therapeutic landscape may be limited (gene therapy, enzyme replacement)
+
+### Polygenic Diseases
+- Many weak genetic signals
+- GWAS provides the gene list
+- Pathway enrichment reveals convergent biology
+- Network analysis identifies hub genes
+
+### Tissue Ambiguity
+- Diseases affecting multiple tissues
+- Query HPA for all relevant tissues
+- Compare tissue-specific expression patterns
+- Use tissue context from disease ontology
+
+---
+
+## Fallback Strategies
+
+### If disease name not found
+1. Try synonyms
+2. Try broader disease category
+3. Try OMIM/UMLS ID mapping
+4. Report disambiguation failure and ask user
+
+### If no GWAS data
+1. Check ClinVar for rare variants
+2. Use OpenTargets genetic evidence
+3. Note in report as "Limited genetic data"
+4. Adjust confidence score accordingly
+
+### If no expression data
+1. Try different disease name/synonym
+2. Check HPA for individual gene expression
+3. Use OpenTargets expression evidence
+4. Note as "Limited transcriptomics data"
+
+### If no pathway enrichment
+1. Reduce gene list stringency
+2. Try different pathway databases
+3. Map individual genes to pathways via Reactome
+4. Note as "No significant pathway enrichment"
+
+### If no drugs found
+1. Check if disease is rare/orphan
+2. Look for drugs targeting individual genes
+3. Check clinical trials for investigational therapies
+4. Note as "No approved drugs - novel therapeutic opportunity"