@bgicli/bgicli 2.1.1 → 2.2.1

package/data/skills/tooluniverse-spatial-omics-analysis/SKILL.md

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+---
+name: tooluniverse-spatial-omics-analysis
+description: Computational analysis framework for spatial multi-omics data integration. Given spatially variable genes (SVGs), spatial domain annotations, tissue type, and disease context from spatial transcriptomics/proteomics experiments (10x Visium, MERFISH, DBiTplus, SLIDE-seq, etc.), performs comprehensive biological interpretation including pathway enrichment, cell-cell interaction inference, druggable target identification, immune microenvironment characterization, and multi-modal integration. Produces a detailed markdown report with Spatial Omics Integration Score (0-100), domain-by-domain characterization, and validation recommendations. Uses 70+ ToolUniverse tools across 9 analysis phases. Use when users ask about spatial transcriptomics analysis, spatial omics interpretation, tissue heterogeneity, spatial gene expression patterns, tumor microenvironment mapping, tissue zonation, or cell-cell communication from spatial data.
+---
+
+# Spatial Multi-Omics Analysis Pipeline
+
+Comprehensive biological interpretation of spatial omics data. Transforms spatially variable genes (SVGs), domain annotations, and tissue context into actionable biological insights covering pathway enrichment, cell-cell interactions, druggable targets, immune microenvironment, and multi-modal integration.
+
+**KEY PRINCIPLES**:
+1. **Report-first approach** - Create report file FIRST, then populate progressively
+2. **Domain-by-domain analysis** - Characterize each spatial region independently before comparison
+3. **Gene-list-centric** - Analyze user-provided SVGs and marker genes with ToolUniverse databases
+4. **Biological interpretation** - Go beyond statistics to explain biological meaning of spatial patterns
+5. **Disease focus** - Emphasize disease mechanisms and therapeutic opportunities when disease context is provided
+6. **Evidence grading** - Grade all evidence as T1 (human/clinical) to T4 (computational)
+7. **Multi-modal thinking** - Integrate RNA, protein, and metabolite information when available
+8. **Validation guidance** - Suggest experimental validation approaches for key findings
+9. **Source references** - Every statement must cite tool/database source
+10. **Completeness checklist** - Mandatory section showing analysis coverage
+11. **English-first queries** - Always use English terms in tool calls. Respond in user's language
+
+---
+
+## When to Use This Skill
+
+Apply when users:
+- Provide spatially variable genes from spatial transcriptomics experiments
+- Ask about biological interpretation of spatial domains/clusters
+- Need pathway enrichment analysis of spatial gene expression data
+- Want to understand cell-cell interactions from spatial data
+- Ask about tumor microenvironment heterogeneity from spatial omics
+- Need druggable targets in specific spatial regions
+- Ask about tissue zonation patterns (liver, brain, kidney)
+- Want to integrate spatial transcriptomics + proteomics data
+- Ask about immune infiltration patterns from spatial data
+- Need to compare healthy vs disease regions spatially
+- Ask "What pathways are enriched in this tumor core vs tumor margin?"
+- Ask "What cell-cell interactions occur in this spatial domain?"
+
+**NOT for** (use other skills instead):
+- Single gene interpretation without spatial context -> Use `tooluniverse-target-research`
+- Variant interpretation -> Use `tooluniverse-variant-interpretation`
+- Drug safety profiling -> Use `tooluniverse-adverse-event-detection`
+- Disease-only analysis without spatial data -> Use `tooluniverse-multiomic-disease-characterization`
+- GWAS analysis -> Use `tooluniverse-gwas-*` skills
+- Bulk RNA-seq (non-spatial) -> Use `tooluniverse-systems-biology`
+
+---
+
+## Input Parameters
+
+| Parameter | Required | Description | Example |
+|-----------|----------|-------------|---------|
+| **svgs** | Yes | Spatially variable genes (gene symbols) | `['EGFR', 'CDH1', 'VIM', 'MYC', 'CD3E']` |
+| **tissue_type** | Yes | Tissue/organ type | `brain`, `liver`, `lung`, `breast`, `skin` |
+| **technology** | No | Spatial omics platform used | `10x Visium`, `MERFISH`, `DBiTplus`, `SLIDE-seq` |
+| **disease_context** | No | Disease if applicable | `breast cancer`, `Alzheimer disease`, `liver cirrhosis` |
+| **spatial_domains** | No | Dict mapping domain name to marker genes | `{'Tumor core': ['MYC','EGFR'], 'Stroma': ['VIM','COL1A1']}` |
+| **cell_types** | No | Cell types identified in deconvolution | `['Epithelial', 'T cell', 'Macrophage', 'Fibroblast']` |
+| **proteins** | No | Proteins detected (if multi-modal) | `['CD3', 'CD8', 'PD-L1', 'Ki67']` |
+| **metabolites** | No | Metabolites detected (if SpatialMETA) | `['glutamine', 'lactate', 'ATP']` |
+
+---
+
+## Spatial Omics Integration Score (0-100)
+
+### Score Components
+
+**Data Completeness (0-30 points)**:
+- SVGs provided (>10 genes): 5 points
+- Disease context provided: 5 points
+- Spatial domains defined: 5 points
+- Cell type composition available: 5 points
+- Multi-modal data (protein/metabolite): 5 points
+- Literature context found: 5 points
+
+**Biological Insight (0-40 points)**:
+- Significant pathway enrichment (FDR < 0.05): 10 points
+- Cell-cell interaction predictions: 10 points
+- Disease mechanism identified: 10 points
+- Druggable targets found in disease regions: 10 points
+
+**Evidence Quality (0-30 points)**:
+- Cross-database validation (gene found in 3+ databases): 10 points
+- Clinical validation (approved drugs for spatial targets): 10 points
+- Literature support (PubMed evidence for spatial patterns): 10 points
+
+### Score Interpretation
+
+| Score | Tier | Interpretation |
+|-------|------|----------------|
+| **80-100** | Excellent | Comprehensive spatial characterization, strong biological insights, druggable targets identified |
+| **60-79** | Good | Good pathway and interaction analysis, some disease/therapeutic context |
+| **40-59** | Moderate | Basic enrichment complete, limited spatial domain comparison or interaction analysis |
+| **0-39** | Limited | Minimal data, gene-level annotation only |
+
+### Evidence Grading System
+
+| Tier | Symbol | Criteria | Examples |
+|------|--------|----------|----------|
+| **T1** | [T1] | Direct human evidence, clinical proof | FDA-approved drug for spatial target, validated biomarker |
+| **T2** | [T2] | Experimental evidence | Validated spatial pattern in literature, known ligand-receptor pair |
+| **T3** | [T3] | Computational/database evidence | PPI network prediction, pathway enrichment, expression correlation |
+| **T4** | [T4] | Annotation/prediction only | GO annotation, text-mined association, predicted interaction |
+
+---
+
+## Report Template
+
+Create this file structure at the start: `{tissue}_{disease}_spatial_omics_report.md`
+
+```markdown
+# Spatial Multi-Omics Analysis Report: {Tissue Type}
+
+**Report Generated**: {date}
+**Technology**: {platform}
+**Tissue**: {tissue_type}
+**Disease Context**: {disease or "Normal tissue"}
+**Total SVGs Analyzed**: {count}
+**Spatial Domains**: {count}
+**Spatial Omics Integration Score**: (to be calculated)
+
+---
+
+## Executive Summary
+
+(2-3 sentence synthesis of key spatial findings - fill after all phases complete)
+
+---
+
+## 1. Tissue & Disease Context
+
+### Tissue Information
+| Property | Value | Source |
+|----------|-------|--------|
+| Tissue type | | |
+| Disease | | |
+| Expected cell types | | HPA |
+
+### Disease Identifiers (if applicable)
+| System | ID | Source |
+|--------|-----|--------|
+
+**Sources**: (tools used)
+
+---
+
+## 2. Spatially Variable Gene Characterization
+
+### 2.1 Gene ID Resolution
+| Gene Symbol | Ensembl ID | Entrez ID | UniProt | Function | Source |
+|-------------|------------|-----------|---------|----------|--------|
+
+### 2.2 Tissue Expression Patterns
+| Gene | Tissue Expression | Specificity | Source |
+|------|-------------------|-------------|--------|
+
+### 2.3 Subcellular Localization
+| Gene | Location | Confidence | Source |
+|------|----------|------------|--------|
+
+### 2.4 Disease Associations
+| Gene | Disease | Score | Evidence | Source |
+|------|---------|-------|----------|--------|
+
+**Sources**: (tools used)
+
+---
+
+## 3. Pathway Enrichment Analysis
+
+### 3.1 STRING Functional Enrichment
+| Category | Term | Description | P-value | FDR | Genes | Source |
+|----------|------|-------------|---------|-----|-------|--------|
+
+### 3.2 Reactome Pathway Analysis
+| Pathway ID | Name | P-value | FDR | Genes Found | Total Genes | Source |
+|------------|------|---------|-----|-------------|-------------|--------|
+
+### 3.3 GO Biological Processes
+| GO Term | Description | P-value | FDR | Genes | Source |
+|---------|-------------|---------|-----|-------|--------|
+
+### 3.4 GO Molecular Functions
+| GO Term | Description | P-value | FDR | Genes | Source |
+|---------|-------------|---------|-----|-------|--------|
+
+### 3.5 GO Cellular Components
+| GO Term | Description | P-value | FDR | Genes | Source |
+|---------|-------------|---------|-----|-------|--------|
+
+### Pathway Summary
+- Top enriched pathways:
+- Key biological processes:
+- Spatial pathway implications:
+
+**Sources**: (tools used)
+
+---
+
+## 4. Spatial Domain Characterization
+
+### Domain: {domain_name}
+
+#### Marker Genes
+| Gene | Function | Pathways | Source |
+|------|----------|----------|--------|
+
+#### Enriched Pathways (domain-specific)
+| Pathway | P-value | FDR | Genes | Source |
+|---------|---------|-----|-------|--------|
+
+#### Cell Type Signature
+| Cell Type | Marker Genes Present | Confidence |
+|-----------|---------------------|------------|
+
+#### Biological Interpretation
+(Narrative interpretation of this domain)
+
+(Repeat for each domain)
+
+### 4.N Domain Comparison
+| Feature | Domain 1 | Domain 2 | Domain 3 |
+|---------|----------|----------|----------|
+| Top pathway | | | |
+| Cell types | | | |
+| Disease relevance | | | |
+
+**Sources**: (tools used)
+
+---
+
+## 5. Cell-Cell Interaction Inference
+
+### 5.1 Protein-Protein Interactions (STRING)
+| Protein A | Protein B | Score | Type | Source |
+|-----------|-----------|-------|------|--------|
+
+### 5.2 Ligand-Receptor Pairs
+| Ligand | Receptor | Domain (Ligand) | Domain (Receptor) | Evidence | Source |
+|--------|----------|-----------------|-------------------|----------|--------|
+
+### 5.3 Signaling Pathways
+| Pathway | Components in Data | Spatial Distribution | Source |
+|---------|--------------------|---------------------|--------|
+
+### 5.4 Interaction Network Summary
+- Key interaction hubs:
+- Cross-domain interactions:
+- Predicted cell-cell communication axes:
+
+**Sources**: (tools used)
+
+---
+
+## 6. Disease & Therapeutic Context
+
+### 6.1 Disease Gene Overlap
+| Gene | Disease Association Score | Evidence Type | Source |
+|------|--------------------------|---------------|--------|
+
+### 6.2 Druggable Targets in Spatial Domains
+| Gene | Domain | Tractability | Modality | Approved Drugs | Source |
+|------|--------|-------------|----------|----------------|--------|
+
+### 6.3 Drug Mechanisms Relevant to Spatial Targets
+| Drug | Target | Mechanism | Phase | Source |
+|------|--------|-----------|-------|--------|
+
+### 6.4 Clinical Trials
+| NCT ID | Title | Target Gene | Phase | Status | Source |
+|--------|-------|-------------|-------|--------|--------|
+
+### Therapeutic Summary
+- Druggable genes in disease regions:
+- Approved therapies:
+- Pipeline drugs:
+- Novel opportunities:
+
+**Sources**: (tools used)
+
+---
+
+## 7. Multi-Modal Integration
+
+### 7.1 Protein-RNA Concordance (if protein data available)
+| Gene/Protein | RNA Pattern | Protein Pattern | Concordance | Source |
+|-------------|-------------|-----------------|-------------|--------|
+
+### 7.2 Subcellular Context
+| Gene | mRNA Location (spatial) | Protein Location (HPA) | Concordance | Source |
+|------|------------------------|----------------------|-------------|--------|
+
+### 7.3 Metabolic Context (if metabolomics available)
+| Gene | Metabolic Pathway | Metabolites Detected | Spatial Pattern | Source |
+|------|-------------------|---------------------|-----------------|--------|
+
+**Sources**: (tools used)
+
+---
+
+## 8. Immune Microenvironment (if relevant)
+
+### 8.1 Immune Cell Markers
+| Cell Type | Marker Genes | Spatial Domain | Source |
+|-----------|-------------|----------------|--------|
+
+### 8.2 Immune Checkpoint Expression
+| Checkpoint | Gene | Expression Pattern | Source |
+|------------|------|--------------------|--------|
+
+### 8.3 Tumor-Immune Interface (if cancer)
+| Feature | Finding | Evidence | Source |
+|---------|---------|----------|--------|
+
+### Immune Summary
+- Immune infiltration pattern:
+- Key immune checkpoints:
+- Immunotherapy implications:
+
+**Sources**: (tools used)
+
+---
+
+## 9. Literature & Validation Context
+
+### 9.1 Literature Evidence
+| PMID | Title | Relevance | Year | Source |
+|------|-------|-----------|------|--------|
+
+### 9.2 Known Spatial Patterns
+(Known tissue architecture/zonation from literature)
+
+### 9.3 Validation Recommendations
+| Priority | Gene/Target | Method | Rationale |
+|----------|-------------|--------|-----------|
+| High | | IHC / smFISH | |
+| Medium | | IF / ISH | |
+
+**Sources**: (tools used)
+
+---
+
+## Spatial Omics Integration Score
+
+| Component | Points | Max | Details |
+|-----------|--------|-----|---------|
+| SVGs provided | | 5 | |
+| Disease context | | 5 | |
+| Spatial domains | | 5 | |
+| Cell types | | 5 | |
+| Multi-modal data | | 5 | |
+| Literature context | | 5 | |
+| Pathway enrichment | | 10 | |
+| Cell-cell interactions | | 10 | |
+| Disease mechanism | | 10 | |
+| Druggable targets | | 10 | |
+| Cross-database validation | | 10 | |
+| Clinical validation | | 10 | |
+| Literature support | | 10 | |
+| **TOTAL** | | **100** | |
+
+**Score**: XX/100 - [Tier]
+
+---
+
+## Completeness Checklist
+
+- [ ] Gene ID resolution complete
+- [ ] Tissue expression patterns analyzed (HPA)
+- [ ] Subcellular localization checked (HPA)
+- [ ] Pathway enrichment complete (STRING + Reactome)
+- [ ] GO enrichment complete (BP + MF + CC)
+- [ ] Spatial domains characterized individually
+- [ ] Domain comparison performed
+- [ ] Protein-protein interactions analyzed (STRING)
+- [ ] Ligand-receptor pairs identified
+- [ ] Disease associations checked (OpenTargets)
+- [ ] Druggable targets identified (OpenTargets tractability)
+- [ ] Drug mechanisms reviewed
+- [ ] Multi-modal integration performed (if data available)
+- [ ] Immune microenvironment characterized (if relevant)
+- [ ] Literature search completed
+- [ ] Validation recommendations provided
+- [ ] Spatial Omics Integration Score calculated
+- [ ] Executive summary written
+- [ ] All sections have source citations
+
+---
+
+## References
+
+### Data Sources Used
+| # | Tool | Parameters | Section | Items Retrieved |
+|---|------|------------|---------|-----------------|
+
+### Database Versions
+- OpenTargets: (current)
+- STRING: v12.0
+- Reactome: (current)
+- HPA: (current)
+- GTEx: v10
+```
+
+---
+
+## Phase 0: Input Processing & Disambiguation (ALWAYS FIRST)
+
+**Objective**: Parse user input, resolve tissue/disease identifiers, establish analysis context.
+
+### Tools Used
+
+**OpenTargets_get_disease_id_description_by_name** (if disease context provided):
+- **Input**: `diseaseName` (string) - Disease name
+- **Output**: `{data: {search: {hits: [{id, name, description}]}}}`
+- **Use**: Get MONDO/EFO IDs for disease queries
+
+**OpenTargets_get_disease_description_by_efoId**:
+- **Input**: `efoId` (string) - Disease ID (e.g., `MONDO_0007254`)
+- **Output**: `{data: {disease: {id, name, description, dbXRefs}}}`
+- **Use**: Get full disease description
+
+**HPA_search_genes_by_query** (tissue cell type context):
+- **Input**: `query` (string) - Search term
+- **Output**: List of gene entries matching query
+- **Use**: Verify tissue-relevant genes
+
+### Workflow
+
+1. Parse SVG list from user input (ensure valid gene symbols)
+2. Identify tissue type and map to standard ontology term
+3. If disease provided, resolve to MONDO/EFO ID using OpenTargets
+4. Get disease description and cross-references
+5. Determine analysis scope:
+   - Cancer? -> Include immune microenvironment, somatic mutations, druggable targets
+   - Neurological? -> Include brain region specificity, neuronal markers
+   - Metabolic? -> Include metabolic zonation, enzyme distribution
+   - Normal tissue? -> Focus on tissue architecture and cell type composition
+6. Set up report file with header information
+
+### Decision Logic
+
+- **Cancer tissue**: Enable immune microenvironment phase, CIViC/cBioPortal queries, immuno-oncology analysis
+- **Normal tissue**: Skip disease phases, focus on tissue zonation and cell type composition
+- **Liver/kidney/brain**: Enable zonation-specific analysis
+- **No disease context**: Proceed with tissue biology only
+- **Small gene list (<20)**: Warn about limited enrichment power, emphasize gene-level analysis
+- **Large gene list (>500)**: Suggest filtering to top SVGs by significance before enrichment
+
+---
+
+## Phase 1: Gene Characterization
+
+**Objective**: Resolve gene identifiers, annotate functions, tissue specificity, and subcellular localization.
+
+### Tools Used
+
+**MyGene_query_genes** (gene ID resolution):
+- **Input**: `query` (string) - Gene symbol
+- **Output**: `{hits: [{_id, symbol, name, ensembl: {gene}, entrezgene}]}`
+- **Use**: Resolve gene symbol to Ensembl ID, Entrez ID
+- **NOTE**: First hit may not be exact match - filter by `symbol` field
+
+**UniProt_get_function_by_accession** (gene function):
+- **Input**: `accession` (string) - UniProt accession
+- **Output**: List of function description strings
+- **Use**: Get protein function annotation
+
+**UniProt_get_subcellular_location_by_accession** (protein localization):
+- **Input**: `accession` (string)
+- **Output**: Subcellular location information
+- **Use**: Where the protein is located in the cell
+
+**HPA_get_subcellular_location** (validated localization):
+- **Input**: `gene_name` (string) - Gene symbol
+- **Output**: `{gene_name, main_locations: [], additional_locations: [], location_summary}`
+- **Use**: Experimentally validated protein subcellular location
+
+**HPA_get_rna_expression_by_source** (tissue expression):
+- **Input**: `gene_name` (string), `source_type` (string: 'tissue'), `source_name` (string)
+- **Output**: `{data: {gene_name, source_type, source_name, expression_value, expression_level}}`
+- **Use**: Check expression in the specific tissue of interest
+- **NOTE**: All 3 parameters are REQUIRED
+
+**HPA_get_comprehensive_gene_details_by_ensembl_id** (full HPA data):
+- **Input**: `ensembl_id` (string), `include_isoforms` (bool), `include_images` (bool), `include_antibodies` (bool), `include_expression` (bool) - ALL 5 parameters REQUIRED
+- **Output**: `{ensembl_id, gene_name, uniprot_ids, summary, protein_classes, tissue_expression, cell_line_expression, ...}`
+- **Use**: One-stop gene characterization from HPA
+- **NOTE**: Use `include_expression=True` for tissue data; set others to `False` for faster response
+
+**HPA_get_cancer_prognostics_by_gene** (cancer prognosis):
+- **Input**: `ensembl_id` (string) - Ensembl gene ID (NOT gene_name)
+- **Output**: `{gene_name, prognostic_cancers_count, prognostic_summary: [{cancer_type, prognostic_type, p_value}]}`
+- **Use**: Prognostic significance in cancer (if cancer context)
+
+**UniProtIDMap_gene_to_uniprot** (ID mapping):
+- **Input**: `gene_name` (string), `organism` (string, default 'human')
+- **Output**: UniProt accession for the gene
+- **Use**: Map gene symbol to UniProt accession
+
+### Workflow
+
+1. For each SVG (batch if >20, sample top genes):
+   a. Query MyGene to get Ensembl ID, Entrez ID
+   b. Map to UniProt accession
+   c. Get subcellular location from HPA
+   d. Get tissue expression from HPA
+   e. If cancer: check cancer prognostics
+2. Compile gene characterization table
+3. Identify genes with tissue-specific expression
+4. Note genes with nuclear vs membrane vs secreted localization (relevant for spatial patterns)
+
+### Batch Strategy for Large Gene Lists
+
+- **10-50 genes**: Characterize all individually
+- **50-200 genes**: Characterize top 50 by priority (known disease genes first), summarize rest
+- **200+ genes**: Characterize top 30, use enrichment for the full list
+- Always run pathway enrichment on the FULL list regardless
+
+---
+
+## Phase 2: Pathway & Functional Enrichment
+
+**Objective**: Identify biological pathways and functions enriched in SVGs and per-domain gene sets.
+
+### Tools Used
+
+**STRING_functional_enrichment** (primary enrichment):
+- **Input**: `protein_ids` (array of gene symbols), `species` (int, 9606 for human)
+- **Output**: `{status: 'success', data: [{category, term, number_of_genes, number_of_genes_in_background, p_value, fdr, description, inputGenes, preferredNames}]}`
+- **Use**: Comprehensive enrichment across GO, KEGG, Reactome, COMPARTMENTS, DISEASES
+- **Categories**: `Process` (GO:BP), `Function` (GO:MF), `Component` (GO:CC), `KEGG`, `Reactome`, `COMPARTMENTS`, `DISEASES`, `Keyword`, `PMID`
+- **NOTE**: This is the PRIMARY enrichment tool. Returns all categories in one call
+
+**ReactomeAnalysis_pathway_enrichment** (Reactome-specific):
+- **Input**: `identifiers` (string, space-separated gene symbols, NOT array)
+- **Output**: `{data: {token, pathways_found, pathways: [{pathway_id, name, p_value, fdr, entities_found, entities_total}]}}`
+- **Use**: Detailed Reactome pathway analysis with hierarchy
+- **NOTE**: identifiers is a SPACE-SEPARATED STRING, not array
+
+**Reactome_map_uniprot_to_pathways** (individual gene):
+- **Input**: `id` (string) - UniProt accession
+- **Output**: Plain list of pathway objects (no data wrapper)
+- **Use**: Map individual proteins to Reactome pathways
+
+**GO_get_annotations_for_gene** (individual gene GO):
+- **Input**: `gene_id` (string) - Gene symbol or ID
+- **Output**: Plain list of GO annotation objects
+- **Use**: Get GO annotations for individual genes
+
+**kegg_search_pathway** (KEGG pathway search):
+- **Input**: `query` (string) - Pathway name or keyword
+- **Output**: Pathway search results
+- **Use**: Find KEGG pathways relevant to spatial findings
+
+**WikiPathways_search** (WikiPathways):
+- **Input**: `query` (string) - Search term
+- **Output**: WikiPathways search results
+- **Use**: Additional pathway context
+
+### Workflow
+
+1. **Global SVG enrichment**: Run STRING_functional_enrichment on ALL SVGs
+   - Filter results by FDR < 0.05
+   - Separate by category (Process, Function, Component, KEGG, Reactome)
+   - Report top 10-15 per category
+2. **Reactome detailed analysis**: Run ReactomeAnalysis_pathway_enrichment
+   - Report top pathways with FDR < 0.05
+3. **Per-domain enrichment** (if spatial domains provided):
+   - Run STRING_functional_enrichment on each domain's gene set
+   - Compare enriched pathways across domains
+   - Identify domain-specific vs shared pathways
+4. **Compile pathway tables**: Merge results from all enrichment tools
+
+### Enrichment Interpretation
+
+- **Signaling pathways** (RTK, Wnt, Notch, Hedgehog): Cell-cell communication
+- **Metabolic pathways**: Tissue metabolic zonation
+- **Immune pathways**: Immune infiltration/exclusion
+- **ECM/adhesion pathways**: Tissue structure and remodeling
+- **Cell cycle/proliferation**: Growth zones
+- **Apoptosis/stress**: Damage zones
+
+---
+
+## Phase 3: Spatial Domain Characterization
+
+**Objective**: Characterize each spatial domain biologically and compare between domains.
+
+### Tools Used
+
+Uses the same tools as Phase 2 (STRING_functional_enrichment, ReactomeAnalysis) applied per-domain, plus:
+
+**HPA_get_biological_processes_by_gene** (per-gene processes):
+- **Input**: `gene_name` (string)
+- **Output**: Biological processes associated with the gene
+- **Use**: Annotate domain marker genes
+
+**HPA_get_protein_interactions_by_gene** (gene interactions):
+- **Input**: `gene_name` (string)
+- **Output**: Known protein interaction partners
+- **Use**: Build domain-specific interaction context
+
+### Workflow
+
+1. For each spatial domain:
+   a. Get marker gene list
+   b. Run STRING_functional_enrichment on domain genes
+   c. Identify top pathways, GO terms
+   d. Assign likely cell type(s) based on marker genes:
+      - Epithelial: CDH1, EPCAM, KRT18, KRT19
+      - Mesenchymal/Fibroblast: VIM, COL1A1, COL3A1, FAP, ACTA2
+      - Immune T cell: CD3E, CD3D, CD4, CD8A, CD8B
+      - Immune B cell: CD19, CD20 (MS4A1), CD79A
+      - Macrophage: CD68, CD163, CSF1R
+      - Endothelial: PECAM1, VWF, CDH5
+      - Neuronal: SNAP25, SYP, MAP2, NEFL
+      - Hepatocyte: ALB, HNF4A, CYP3A4
+   e. Generate biological interpretation narrative
+2. Compare domains:
+   - Differential pathways
+   - Unique vs shared genes
+   - Disease-relevant vs homeostatic regions
+   - Transition zones (shared genes between adjacent domains)
+
+### Cell Type Assignment Rules
+
+When user does not provide cell type annotations, infer from marker genes:
+- Check each gene against known cell type markers
+- Use HPA tissue/cell type expression data for validation
+- Report confidence level (high: 3+ markers match, medium: 2 markers, low: 1 marker)
+
+---
+
+## Phase 4: Cell-Cell Interaction Inference
+
+**Objective**: Predict cell-cell communication from spatial gene expression patterns.
+
+### Tools Used
+
+**STRING_get_interaction_partners** (PPI network):
+- **Input**: `protein_ids` (array), `species` (int, 9606), `limit` (int), `confidence_score` (float, 0.7)
+- **Output**: `{status: 'success', data: [{preferredName_A, preferredName_B, score, nscore, fscore, pscore, ascore, escore, dscore, tscore}]}`
+- **Use**: Find protein-protein interactions among SVGs
+- **Score types**: nscore=neighborhood, fscore=fusion, pscore=phylogenetic, ascore=coexpression, escore=experimental, dscore=database, tscore=textmining
+
+**STRING_get_protein_interactions** (pairwise interactions):
+- **Input**: `protein_ids` (array), `species` (int, 9606)
+- **Output**: Interaction data between specified proteins
+- **Use**: Get interactions within a specific gene set
+
+**intact_search_interactions** (IntAct database):
+- **Input**: `query` (string), `max` (int)
+- **Output**: Interaction data from IntAct
+- **Use**: Complement STRING with IntAct interactions
+
+**Reactome_get_interactor** (Reactome interactions):
+- **Input**: Protein/gene identifier
+- **Output**: Reactome interaction data
+- **Use**: Pathway-level interaction context
+
+**DGIdb_get_drug_gene_interactions** (drug-gene interactions):
+- **Input**: `genes` (array of strings)
+- **Output**: Drug-gene interaction data
+- **Use**: Identify druggable interaction nodes
+
+### Ligand-Receptor Analysis
+
+Known ligand-receptor pairs to check in SVG list:
+- **Growth factors**: EGF-EGFR, HGF-MET, VEGF-KDR, FGF-FGFR, PDGF-PDGFRA/B
+- **Cytokines**: TNF-TNFR, IL6-IL6R, IFNG-IFNGR, TGFB1-TGFBR1/2
+- **Chemokines**: CXCL12-CXCR4, CCL2-CCR2, CXCL10-CXCR3
+- **Immune checkpoints**: CD274(PD-L1)-PDCD1(PD-1), CD80/CD86-CTLA4, LGALS9-HAVCR2(TIM-3)
+- **Notch signaling**: DLL1/3/4-NOTCH1/2/3/4, JAG1/2-NOTCH1/2
+- **Wnt signaling**: WNT ligands-FZD receptors
+- **Adhesion**: CDH1-CDH1 (homotypic), ITGA/B integrins-ECM
+- **Hedgehog**: SHH-PTCH1
+
+### Workflow
+
+1. Run STRING_get_interaction_partners on all SVGs
+   - Filter interactions with score > 0.7
+   - Identify hub genes (most connections)
+2. Check for known ligand-receptor pairs in gene list
+   - Cross-reference with spatial domain assignments
+   - Identify potential cross-domain signaling
+3. Build interaction network:
+   - Intra-domain interactions (within same spatial region)
+   - Inter-domain interactions (between different regions)
+   - Identify signaling axes (e.g., tumor-stroma, immune-tumor)
+4. Map interactions to Reactome signaling pathways
+
+---
+
+## Phase 5: Disease & Therapeutic Context
+
+**Objective**: Connect spatial findings to disease mechanisms and identify druggable targets.
+
+### Tools Used
+
+**OpenTargets_get_associated_targets_by_disease_efoId** (disease genes):
+- **Input**: `efoId` (string), `size` (int)
+- **Output**: `{data: {disease: {associatedTargets: {count, rows: [{target: {id, approvedSymbol}, score}]}}}}`
+- **Use**: Get disease-associated genes, overlap with SVGs
+
+**OpenTargets_get_target_tractability_by_ensemblID** (druggability):
+- **Input**: `ensemblId` (string)
+- **Output**: Tractability data (small molecule, antibody, other modalities)
+- **Use**: Assess if spatial targets are druggable
+
+**OpenTargets_get_associated_drugs_by_target_ensemblID** (drugs for target):
+- **Input**: `ensemblId` (string), `size` (int)
+- **Output**: Drug data for the target
+- **Use**: Find approved/clinical drugs targeting spatial genes
+
+**OpenTargets_get_drug_mechanisms_of_action_by_chemblId** (drug mechanism):
+- **Input**: `chemblId` (string)
+- **Output**: Mechanism of action data
+- **Use**: Understand how drugs act on spatial targets
+
+**OpenTargets_target_disease_evidence** (evidence linking target to disease):
+- **Input**: `ensemblId` (string), `efoId` (string)
+- **Output**: Evidence items linking target to disease
+- **Use**: Specific evidence for each spatial gene in disease
+
+**clinical_trials_search** (clinical trials):
+- **Input**: `action` = `"search_studies"`, `condition` (string), `intervention` (string), `limit` (int)
+- **Output**: `{total_count, studies: [{nctId, title, status, conditions}]}`
+- **Use**: Find clinical trials for spatial targets
+- **NOTE**: `action` MUST be `"search_studies"`
+
+**DGIdb_get_gene_druggability** (druggability categories):
+- **Input**: `genes` (array of strings)
+- **Output**: `{data: {genes: {nodes: [{name, geneCategories: [{name}]}]}}}`
+- **Use**: Classify genes as druggable, kinase, GPCR, etc.
+
+**civic_search_genes** (CIViC cancer evidence, if cancer):
+- **Input**: (no filter by name)
+- **Output**: Gene list from CIViC
+- **Use**: Check if SVGs have CIViC clinical evidence
+
+### Workflow
+
+1. **Disease gene overlap** (if disease context provided):
+   a. Get disease-associated targets from OpenTargets
+   b. Intersect with SVGs
+   c. For overlapping genes, get specific evidence
+2. **Druggable target identification**:
+   a. Run DGIdb_get_gene_druggability on all SVGs
+   b. For druggable genes, check OpenTargets tractability
+   c. Get approved drugs for druggable spatial targets
+3. **Clinical trials**:
+   a. Search for trials targeting spatial genes in the disease context
+   b. Prioritize trials for genes in disease-enriched spatial domains
+4. **Cancer-specific** (if cancer):
+   a. Check CIViC for clinical evidence
+   b. Get mutation prevalence from cBioPortal (if specific mutations known)
+   c. Check immune checkpoint genes in spatial data
+
+---
+
+## Phase 6: Multi-Modal Integration
+
+**Objective**: Integrate protein, RNA, and metabolite spatial data when available.
+
+### Tools Used
+
+**HPA_get_subcellular_location** (protein localization):
+- **Input**: `gene_name` (string)
+- **Output**: `{gene_name, main_locations, additional_locations, location_summary}`
+- **Use**: Compare mRNA spatial pattern with protein subcellular location
+
+**HPA_get_rna_expression_in_specific_tissues** (tissue RNA):
+- **Input**: `ensembl_id` (string), `tissue_name` (string)
+- **Output**: Expression data for specific tissue
+- **Use**: Validate spatial expression against bulk tissue data
+
+**Reactome_map_uniprot_to_pathways** (metabolic pathways):
+- **Input**: `id` (string) - UniProt accession
+- **Output**: List of pathways
+- **Use**: Map genes to metabolic pathways for metabolomics integration
+
+**kegg_get_pathway_info** (KEGG pathway details):
+- **Input**: `pathway_id` (string) - KEGG pathway ID
+- **Output**: Pathway information including metabolites
+- **Use**: Link spatial genes to metabolic pathways and metabolites
+
+### Workflow
+
+1. **RNA-Protein concordance** (if protein data provided):
+   a. For each gene with both RNA and protein data:
+      - Compare spatial RNA pattern with protein detection
+      - Check HPA for known post-transcriptional regulation
+      - Note concordant (expected) vs discordant (interesting) patterns
+2. **Subcellular context**:
+   a. Map spatial RNA localization to protein subcellular location (HPA)
+   b. Secreted proteins -> likely paracrine signaling
+   c. Membrane proteins -> cell surface markers
+   d. Nuclear proteins -> transcription factors
+3. **Metabolic integration** (if metabolomics available):
+   a. Map genes to metabolic pathways (Reactome, KEGG)
+   b. Link detected metabolites to enzyme-encoding genes
+   c. Identify spatial metabolic heterogeneity
+   d. Check for known metabolic zonation patterns
+
+---
+
+## Phase 7: Immune Microenvironment (Cancer/Inflammation)
+
+**Objective**: Characterize immune cell composition and checkpoint expression in spatial context.
+
+### Conditions for Activation
+
+Only execute if:
+- Disease context is cancer, autoimmune, or inflammatory
+- SVGs include immune markers (CD3E, CD8A, CD68, CD163, etc.)
+- User specifically asks about immune patterns
+
+### Tools Used
+
+**STRING_functional_enrichment** (immune pathway enrichment):
+- Applied to immune-relevant SVGs
+- Filter for immune-related GO terms and pathways
+
+**OpenTargets_get_target_tractability_by_ensemblID** (checkpoint druggability):
+- Applied to immune checkpoint genes
+- Check for approved immunotherapies
+
+**iedb_search_epitopes** (epitope data):
+- **Input**: `organism_name` (string), `source_antigen_name` (string)
+- **Output**: `{status, data, count}`
+- **Use**: Check if spatial antigens have known epitopes
+
+### Immune Cell Markers Reference
+
+| Cell Type | Key Markers | Extended Markers |
+|-----------|-------------|-----------------|
+| CD8+ T cell | CD8A, CD8B | GZMA, GZMB, PRF1, IFNG |
+| CD4+ T cell | CD4 | IL2, IL4, IL17A, FOXP3 (Treg) |
+| Regulatory T cell | FOXP3, IL2RA | CTLA4, TIGIT |
+| B cell | CD19, MS4A1, CD79A | IGHG1, IGHM |
+| Plasma cell | SDC1 (CD138), XBP1 | IGHG1, MZB1 |
+| M1 Macrophage | CD68, NOS2, TNF | IL1B, CXCL10 |
+| M2 Macrophage | CD68, CD163, MRC1 | ARG1, IL10 |
+| Dendritic cell | ITGAX (CD11c), HLA-DRA | CD80, CD86 |
+| NK cell | NCAM1 (CD56), NKG7 | GNLY, KLRD1 |
+| Neutrophil | FCGR3B, CXCR2 | S100A8, S100A9 |
+| Mast cell | KIT, TPSAB1 | CPA3, HDC |
+
+### Immune Checkpoint Reference
+
+| Checkpoint | Gene | Ligand | Therapeutic Antibody |
+|------------|------|--------|---------------------|
+| PD-1/PD-L1 | PDCD1/CD274 | CD274, PDCD1LG2 | Pembrolizumab, Nivolumab, Atezolizumab |
+| CTLA-4 | CTLA4 | CD80, CD86 | Ipilimumab |
+| TIM-3 | HAVCR2 | LGALS9 | Sabatolimab |
+| LAG-3 | LAG3 | HLA class II | Relatlimab |
+| TIGIT | TIGIT | PVR, PVRL2 | Tiragolumab |
+| VISTA | VSIR | PSGL1 | - |
+
+### Workflow
+
+1. Identify immune-related SVGs from marker reference
+2. Classify immune cell types present per spatial domain
+3. Check immune checkpoint expression
+4. Assess immune infiltration patterns:
+   - Hot (T cell infiltrated) vs Cold (immune desert) vs Excluded
+5. Identify potential immunotherapy targets
+6. Check for tertiary lymphoid structures (B cell + T cell clusters)
+
+---
+
+## Phase 8: Literature & Validation Context
+
+**Objective**: Provide literature evidence for spatial findings and suggest validation experiments.
+
+### Tools Used
+
+**PubMed_search_articles** (literature search):
+- **Input**: `query` (string), `max_results` (int)
+- **Output**: List of `[{pmid, title, authors, journal, pub_date, doi}]`
+- **Use**: Find published evidence for spatial patterns
+
+**openalex_literature_search** (broader literature):
+- **Input**: `query` (string), `per_page` (int)
+- **Output**: List of works with titles, DOIs, abstracts
+- **Use**: Complement PubMed with preprints and broader coverage
+
+### Literature Search Strategy
+
+1. **Tissue + spatial**: `"{tissue} spatial transcriptomics"` - e.g., "liver spatial transcriptomics"
+2. **Disease + spatial**: `"{disease} spatial omics"` - e.g., "breast cancer spatial transcriptomics"
+3. **Gene + tissue**: `"{top_gene} {tissue} expression"` for key SVGs
+4. **Zonation** (if relevant): `"{tissue} zonation gene expression"`
+5. **Technology**: `"{technology} {tissue}"` - e.g., "Visium breast cancer"
+
+### Validation Recommendations Template
+
+| Priority | Target | Method | Rationale | Feasibility |
+|----------|--------|--------|-----------|-------------|
+| **High** | Key SVG | smFISH / RNAscope | Validate spatial pattern at single-molecule level | Medium |
+| **High** | Druggable target | IHC on serial sections | Confirm protein expression in spatial domain | High |
+| **High** | Ligand-receptor pair | Proximity ligation assay (PLA) | Confirm physical interaction at tissue level | Medium |
+| **Medium** | Domain markers | Multiplexed IF (CODEX/IBEX) | Validate multiple markers simultaneously | Low-Medium |
+| **Medium** | Pathway | Spatial metabolomics (MALDI/DESI) | Confirm metabolic pathway activity | Low |
+| **Low** | Novel interaction | Co-culture + conditioned media | Functional validation of predicted interaction | Medium |
+
+### Workflow
+
+1. Search PubMed for tissue + disease + spatial transcriptomics
+2. Search for known spatial patterns in the tissue type
+3. Cross-reference findings with published spatial atlas data
+4. Generate validation recommendations based on:
+   - Novelty of finding (novel patterns need more validation)
+   - Clinical relevance (druggable targets prioritized)
+   - Technical feasibility
+5. Cite relevant methodology papers for each validation approach
+
+---
+
+## Tool Parameter Reference (CRITICAL)
+
+### Verified Parameter Names
+
+| Tool | Parameter | CORRECT | Common MISTAKE | Notes |
+|------|-----------|---------|----------------|-------|
+| `MyGene_query_genes` | query | `query` | `q` | Filter results by `symbol` field |
+| `STRING_functional_enrichment` | identifiers | `protein_ids` (array) | `identifiers` | Also needs `species=9606` |
+| `STRING_get_interaction_partners` | identifiers | `protein_ids` (array) | `identifiers` | `limit`, `confidence_score` optional |
+| `ReactomeAnalysis_pathway_enrichment` | genes | `identifiers` (string) | Array | SPACE-SEPARATED string, NOT array |
+| `HPA_get_subcellular_location` | gene | `gene_name` | `ensembl_id` | Uses gene symbol |
+| `HPA_get_cancer_prognostics_by_gene` | gene | `ensembl_id` | `gene_name` | Uses Ensembl ID, NOT symbol |
+| `HPA_get_rna_expression_by_source` | params | `gene_name`, `source_type`, `source_name` | - | ALL 3 required |
+| `HPA_get_rna_expression_in_specific_tissues` | gene | `ensembl_id` | `gene_name` | Uses Ensembl ID |
+| `OpenTargets_get_target_tractability_by_ensemblID` | target | `ensemblId` | `ensemblID` | camelCase |
+| `OpenTargets_get_associated_drugs_by_target_ensemblID` | target | `ensemblId`, `size` | - | Both REQUIRED |
+| `OpenTargets_get_associated_targets_by_disease_efoId` | disease | `efoId` | `diseaseId` | Returns {data: {disease: {associatedTargets}}} |
+| `DGIdb_get_gene_druggability` | genes | `genes` (array) | `gene_name` | Array of strings |
+| `DGIdb_get_drug_gene_interactions` | genes | `genes` (array) | `gene_name` | Array of strings |
+| `clinical_trials_search` | action | `action='search_studies'` | Missing action | `action` is REQUIRED |
+| `ensembl_lookup_gene` | species | `species='homo_sapiens'` | No species | REQUIRED parameter |
+| GTEx tools | operation | `operation` (SOAP) | Missing | All GTEx tools need `operation` parameter |
+| `HPA_get_comprehensive_gene_details_by_ensembl_id` | all params | ALL 5 required: `ensembl_id`, `include_isoforms`, `include_images`, `include_antibodies`, `include_expression` | Missing booleans | Set booleans to False except expression |
+| GTEx tools | gencode | `gencode_id` (array) | `gene_id` | Requires versioned GENCODE ID |
+
+### Response Format Reference
+
+| Tool | Response Format | Key Fields |
+|------|----------------|------------|
+| `STRING_functional_enrichment` | `{status, data: [{category, term, description, p_value, fdr, inputGenes}]}` | Filter by FDR < 0.05 |
+| `ReactomeAnalysis_pathway_enrichment` | `{data: {pathways: [{pathway_id, name, p_value, fdr, entities_found, entities_total}]}}` | Top 20 returned |
+| `STRING_get_interaction_partners` | `{status, data: [{preferredName_A, preferredName_B, score}]}` | Score > 0.7 for high confidence |
+| `MyGene_query_genes` | `{hits: [{_id, symbol, name, ensembl: {gene}, entrezgene}]}` | Filter by exact symbol match |
+| `HPA_get_subcellular_location` | `{gene_name, main_locations: [], additional_locations: [], location_summary}` | Direct dict response |
+| `OpenTargets_get_target_tractability_by_ensemblID` | `{data: {target: {id, tractability: [{label, modality, value}]}}}` | Check value=true |
+| `DGIdb_get_gene_druggability` | `{data: {genes: {nodes: [{name, geneCategories: [{name}]}]}}}` | GraphQL response |
+| `PubMed_search_articles` | Plain list of `[{pmid, title, authors, journal, pub_date}]` | No data wrapper |
+| `clinical_trials_search` | `{total_count, studies: [{nctId, title, status, conditions}]}` | total_count can be None |
+
+---
+
+## Fallback Strategies
+
+### Pathway Enrichment
+- **Primary**: STRING_functional_enrichment (most comprehensive, one call)
+- **Fallback**: ReactomeAnalysis_pathway_enrichment (Reactome-specific)
+- **Default**: Individual gene GO annotations (GO_get_annotations_for_gene)
+
+### Tissue Expression
+- **Primary**: HPA_get_rna_expression_by_source
+- **Fallback**: HPA_get_comprehensive_gene_details_by_ensembl_id
+- **Default**: Note "tissue expression data unavailable"
+
+### Disease Association
+- **Primary**: OpenTargets_get_associated_targets_by_disease_efoId
+- **Fallback**: OpenTargets_target_disease_evidence (per gene)
+- **Default**: Skip disease section if no disease context
+
+### Drug Information
+- **Primary**: OpenTargets_get_associated_drugs_by_target_ensemblID
+- **Fallback**: DGIdb_get_drug_gene_interactions
+- **Default**: Note "no approved drugs identified"
+
+### Literature
+- **Primary**: PubMed_search_articles
+- **Fallback**: openalex_literature_search
+- **Default**: Note "no spatial-specific literature found"
+
+---
+
+## Common Use Cases
+
+### Use Case 1: Cancer Spatial Heterogeneity
+
+**Input**: Visium data from breast cancer with 5 spatial domains (tumor core, tumor margin, stroma, immune infiltrate, normal tissue) and 200 SVGs.
+
+**Analysis focus**:
+- Tumor-specific pathways (proliferation, DNA repair)
+- Immune infiltration patterns (hot vs cold)
+- Tumor-stroma interactions (CAF signaling)
+- Druggable targets in tumor core
+- Immune checkpoint expression patterns
+- Prognostic genes per domain
+
+### Use Case 2: Brain Tissue Zonation
+
+**Input**: MERFISH data from hippocampus with cell-type specific genes and neuronal subtype markers.
+
+**Analysis focus**:
+- Neuronal subtype characterization
+- Synaptic signaling pathways
+- Neurotransmitter receptor distribution
+- Known hippocampal zonation patterns (CA1, CA3, DG)
+- Neurodegenerative disease gene overlap
+
+### Use Case 3: Liver Metabolic Zonation
+
+**Input**: Spatial transcriptomics of liver with periportal vs pericentral gene gradients.
+
+**Analysis focus**:
+- Metabolic enzyme distribution (CYP450, gluconeogenesis, lipogenesis)
+- Wnt signaling gradient (known zonation regulator)
+- Oxygen gradient-responsive genes
+- Drug metabolism enzyme spatial patterns
+- Liver disease gene overlap
+
+### Use Case 4: Tumor-Immune Interface
+
+**Input**: DBiTplus data from melanoma with spatial protein + RNA data showing tumor-immune boundary.
+
+**Analysis focus**:
+- Immune cell composition at boundary
+- Checkpoint ligand-receptor pairs
+- Immune exclusion mechanisms
+- Immunotherapy target identification
+- Multi-modal (RNA + protein) concordance
+
+### Use Case 5: Developmental Spatial Patterns
+
+**Input**: Spatial transcriptomics of embryonic tissue with developmental patterning genes.
+
+**Analysis focus**:
+- Morphogen gradients (Wnt, BMP, FGF, SHH)
+- Transcription factor spatial patterns
+- Cell fate determination genes
+- Developmental signaling pathways
+- Comparison to adult tissue patterns
+
+### Use Case 6: Disease Progression Mapping
+
+**Input**: Spatial data from neurodegenerative tissue showing disease gradient from affected to unaffected regions.
+
+**Analysis focus**:
+- Disease gene expression gradient
+- Inflammatory response spatial pattern
+- Neuronal loss markers
+- Glial activation patterns
+- Therapeutic window identification
+
+---
+
+## Limitations & Known Issues
+
+### Database-Specific
+- **Enrichment**: `enrichr_gene_enrichment_analysis` returns connectivity graph (107MB), NOT standard enrichment. Use `STRING_functional_enrichment` instead
+- **GTEx**: SOAP-style tools requiring `operation` parameter; needs versioned GENCODE IDs (e.g., `ENSG00000141510.16`)
+- **HPA**: Some tools use `gene_name`, others use `ensembl_id` - check parameter reference
+- **OpenTargets**: Disease IDs use underscore format (`MONDO_0007254`), not colon
+- **cBioPortal_get_cancer_studies**: BROKEN - has literal `{limit}` in URL causing 400 error
+
+### Conceptual
+- **No raw spatial data processing**: This skill analyzes gene LISTS, not raw spatial matrices (Seurat/Scanpy/squidpy handle raw data)
+- **No spatial statistics**: Cannot perform Moran's I, spatial autocorrelation, or variogram analysis
+- **No image analysis**: Cannot process H&E or fluorescence images
+- **No deconvolution**: Cannot perform cell type deconvolution (use BayesSpace, cell2location, RCTD externally)
+- **Ligand-receptor inference**: Based on gene co-expression + known pairs, not spatial proximity statistics (use CellChat, NicheNet, COMMOT externally)
+
+### Technical
+- **Large gene lists**: >200 genes may slow STRING queries; batch or sample
+- **Response format variability**: Always check both dict and list response types
+- **Rate limits**: STRING and OpenTargets may throttle frequent requests
+
+---
+
+## Summary
+
+Spatial Multi-Omics Analysis skill provides:
+
+1. Gene characterization (ID resolution, function, localization, tissue expression)
+2. Pathway & functional enrichment (STRING, Reactome, GO, KEGG)
+3. Spatial domain characterization (per-domain and cross-domain comparison)
+4. Cell-cell interaction inference (PPI, ligand-receptor, signaling pathways)
+5. Disease & therapeutic context (disease genes, druggable targets, clinical trials)
+6. Multi-modal integration (RNA-protein concordance, metabolic pathways)
+7. Immune microenvironment characterization (cell types, checkpoints, immunotherapy)
+8. Literature context & validation recommendations
+
+**Outputs**: Comprehensive markdown report with Spatial Omics Integration Score (0-100)
+**Best for**: Biological interpretation of spatial omics experiments (post-processing after spatial data analysis tools)
+**Uses**: 70+ ToolUniverse tools across 9 analysis phases
+**Time**: ~10-20 minutes depending on gene list size and analysis scope