USAGE_EXAMPLES.md•2.67 kB
# NCBI Gene MCP Client - Usage Examples
## Installation
```bash
pip install -e .
```
## Quick Start
### 1. Python API Usage
```python
from ncbi_gene_mcp_client.main import NCBIGeneMCPClientBridge
# Initialize client
client = NCBIGeneMCPClientBridge()
# Get gene information
gene_info = client.fetch_gene_info("672") # BRCA1
print(f"Gene: {gene_info.name}")
print(f"Description: {gene_info.description}")
```
### 2. Command Line Usage
```bash
# Demo
ncbi-gene-client demo
# Search for genes
ncbi-gene-client search-genes "BRCA1"
# Get gene information by ID
ncbi-gene-client gene-info 672
# Search by gene symbol
ncbi-gene-client search-symbol BRCA1 --organism human
```
### 3. MCP Server Usage
```bash
# Start the MCP server
ncbi-gene-mcp-server
# The server provides these tools:
# - search_genes
# - fetch_gene_info
# - fetch_protein_info
# - search_by_gene_symbol
```
## NCBI API Best Practices
1. **Provide your email** (recommended by NCBI):
```python
client = NCBIGeneMCPClientBridge(email="your@email.com")
```
2. **Use API key for higher rate limits**:
```python
client = NCBIGeneMCPClientBridge(
email="your@email.com",
api_key="your_ncbi_api_key"
)
```
3. **Rate limiting is automatically handled**:
- Without API key: 3 requests/second
- With API key: 10 requests/second
## Example Use Cases
### Cancer Research - BRCA1 Analysis
```python
# Get BRCA1 gene details
brca1 = client.fetch_gene_info("672")
print(f"BRCA1 is located on chromosome {brca1.chromosome}")
print(f"Map location: {brca1.map_location}")
```
### Cross-Species Comparison
```python
# Compare BRCA1 across species
for organism in ["human", "mouse", "rat"]:
genes = client.search_by_gene_symbol("BRCA1", organism=organism)
if genes:
gene = genes[0]
print(f"{organism}: Chr {gene.chromosome}")
```
### Disease Gene Discovery
```python
# Find genes associated with diabetes
results = client.search_genes("diabetes[disease] AND human[organism]")
print(f"Found {results.count} genes associated with diabetes")
```
## Data Models
### GeneInfo
- `gene_id`: NCBI Gene ID
- `name`: Gene symbol/name
- `description`: Gene description
- `organism`: Scientific name
- `chromosome`: Chromosome location
- `map_location`: Precise location
- `gene_type`: Type of gene
- `other_aliases`: Alternative names
- `summary`: Detailed description
### SearchResult
- `count`: Total number of results
- `ids`: List of gene IDs found
- `query_translation`: How NCBI interpreted the query
## Testing
```bash
# Run basic tests
pytest tests/ -v
# Run integration tests (requires internet)
pytest tests/ -m integration -v
```