# Scientific Features Specification
## Overview
Enhanced scientific capabilities to transform the AGR MCP Server into a comprehensive genomics research platform.
## 🧬 Pathway Analysis
### Implementation
- **KEGG Integration**: Map genes to metabolic and signaling pathways
- **Reactome Integration**: Detailed biochemical reaction networks
- **Gene Ontology**: Enhanced GO term analysis and enrichment
- **Custom Pathways**: User-defined pathway creation and analysis
### API Endpoints
```javascript
// Get pathways for a gene
{
"tool": "get_gene_pathways",
"arguments": {
"gene_id": "HGNC:1100",
"databases": ["kegg", "reactome", "go"],
"include_interactions": true
}
}
// Pathway enrichment analysis
{
"tool": "pathway_enrichment",
"arguments": {
"gene_list": ["BRCA1", "BRCA2", "TP53", "ATM"],
"background": "human_genome",
"p_value_threshold": 0.05
}
}
```
### Natural Language Queries
- "What pathways is BRCA1 involved in?"
- "Find enriched pathways in my gene list"
- "Show DNA repair pathway genes"
## 🧪 Protein Structure Integration
### Implementation
- **PDB Integration**: 3D protein structure data
- **AlphaFold Integration**: Predicted protein structures
- **Domain Analysis**: Protein domain identification and classification
- **Structure-Function Mapping**: Link structural features to biological function
### API Endpoints
```javascript
// Get protein structure information
{
"tool": "get_protein_structure",
"arguments": {
"gene_id": "HGNC:1100",
"structure_source": ["pdb", "alphafold"],
"include_domains": true
}
}
// Structure similarity search
{
"tool": "find_similar_structures",
"arguments": {
"protein_id": "P38398",
"similarity_threshold": 0.8
}
}
```
### Natural Language Queries
- "Show me the 3D structure of BRCA1"
- "Find proteins with similar structure to TP53"
- "What domains does this protein have?"
## 🌳 Phylogenetic Analysis
### Implementation
- **Species Tree**: Evolutionary relationships between organisms
- **Gene Tree**: Evolution of specific gene families
- **Ortholog Groups**: Systematic orthology classification
- **Evolutionary Rates**: Calculate evolutionary distances and substitution rates
### API Endpoints
```javascript
// Generate phylogenetic tree
{
"tool": "build_phylogenetic_tree",
"arguments": {
"gene_family": "BRCA",
"species": ["human", "mouse", "zebrafish", "fly"],
"tree_method": "neighbor_joining"
}
}
// Evolutionary analysis
{
"tool": "analyze_evolution",
"arguments": {
"gene_id": "HGNC:1100",
"include_selection_pressure": true,
"calculate_dn_ds": true
}
}
```
### Natural Language Queries
- "Build a phylogenetic tree for BRCA genes"
- "How did insulin evolve across species?"
- "Show evolutionary relationships of DNA repair genes"
## 🧬 Variant Analysis
### Implementation
- **SNP Impact Prediction**: SIFT, PolyPhen, CADD scores
- **Clinical Significance**: ClinVar integration
- **Population Frequency**: gnomAD population data
- **Structural Variants**: CNV and indel analysis
- **Pharmacogenomics**: Drug response variants
### API Endpoints
```javascript
// Analyze variant impact
{
"tool": "analyze_variant",
"arguments": {
"variant": "chr17:41234451:A>T",
"gene_context": true,
"clinical_significance": true,
"population_frequency": true
}
}
// Variant annotation
{
"tool": "annotate_variants",
"arguments": {
"vcf_data": "variant_list.vcf",
"annotation_sources": ["clinvar", "gnomad", "dbsnp"]
}
}
```
### Natural Language Queries
- "What's the impact of this BRCA1 variant?"
- "Find pathogenic variants in DNA repair genes"
- "Show population frequency of this mutation"
## 💊 Drug-Gene Interactions
### Implementation
- **PharmGKB Integration**: Pharmacogenomic relationships
- **DrugBank Integration**: Drug target information
- **Clinical Trials**: Ongoing drug studies
- **Drug Repurposing**: Alternative therapeutic applications
### API Endpoints
```javascript
// Find drug interactions
{
"tool": "get_drug_interactions",
"arguments": {
"gene_id": "HGNC:1100",
"interaction_types": ["target", "biomarker", "pathway"],
"clinical_phase": "all"
}
}
// Drug repurposing analysis
{
"tool": "find_drug_candidates",
"arguments": {
"disease": "breast cancer",
"gene_targets": ["BRCA1", "BRCA2"],
"mechanism": "DNA repair"
}
}
```
### Natural Language Queries
- "What drugs target BRCA1?"
- "Find cancer drugs that affect DNA repair"
- "Show clinical trials for TP53 modulators"
## 📚 Literature Mining
### Implementation
- **PubMed Integration**: Gene-related scientific literature
- **Text Mining**: Extract gene mentions and relationships
- **Citation Networks**: Track influential papers
- **Knowledge Graphs**: Build relationships from literature
- **Real-time Updates**: Track new publications
### API Endpoints
```javascript
// Literature search
{
"tool": "search_literature",
"arguments": {
"gene_id": "HGNC:1100",
"keywords": ["breast cancer", "DNA repair"],
"date_range": "2020-2024",
"limit": 50
}
}
// Extract gene relationships from literature
{
"tool": "mine_gene_relationships",
"arguments": {
"pmid_list": ["12345678", "87654321"],
"relationship_types": ["interaction", "pathway", "disease"]
}
}
```
### Natural Language Queries
- "Find recent papers about BRCA1 and breast cancer"
- "What genes interact with TP53 according to literature?"
- "Show trending research on DNA repair mechanisms"
## 🔬 Experimental Data Integration
### Implementation
- **Expression Atlas**: Tissue-specific expression patterns
- **ChIP-seq Data**: Transcription factor binding sites
- **ATAC-seq**: Chromatin accessibility
- **Hi-C Data**: 3D genome organization
- **Single-cell Data**: Cell-type specific expression
### API Endpoints
```javascript
// Get experimental data
{
"tool": "get_experimental_data",
"arguments": {
"gene_id": "HGNC:1100",
"data_types": ["expression", "chip_seq", "atac_seq"],
"tissues": ["breast", "ovary", "brain"],
"cell_types": ["epithelial", "fibroblast"]
}
}
// Chromatin analysis
{
"tool": "analyze_chromatin",
"arguments": {
"genomic_region": "chr17:41234451-41244451",
"include_tf_binding": true,
"include_histone_marks": true
}
}
```
### Natural Language Queries
- "Where is BRCA1 expressed in the body?"
- "What transcription factors bind to this promoter?"
- "Show chromatin accessibility for DNA repair genes"
## Implementation Priority
1. **Phase 1** (Immediate): Pathway Analysis + Literature Mining
2. **Phase 2** (Short-term): Variant Analysis + Drug Interactions
3. **Phase 3** (Medium-term): Protein Structure + Experimental Data
4. **Phase 4** (Long-term): Phylogenetic Analysis + Advanced Features
## Technical Requirements
- **External APIs**: KEGG, Reactome, PDB, AlphaFold, PubMed, ClinVar
- **Data Storage**: Enhanced caching for large datasets
- **Processing Power**: Computational requirements for analysis
- **Dependencies**: Bioinformatics libraries (BioPython, etc.)
## Benefits for Researchers
- **Comprehensive Analysis**: One-stop platform for genomic research
- **Time Saving**: Integrated data reduces manual lookup time
- **Discovery**: Find hidden connections between genes, diseases, and drugs
- **Reproducibility**: Standardized analysis workflows
- **Collaboration**: Share and reuse analysis results
