This server does not currently have a deployable release on Glama. Follow the repository's setup instructions to install and configure it for your MCP client, including any required credentials and local dependencies.
MCP (Model Context Protocol) Server for the National Microbiology Data Center (NMDC) of China.
NMDC-MCP is a Model Context Protocol (MCP) server that provides AI applications with access to the data and services of the National Microbiology Data Center (NMDC) — China's national-level data center for microbiology research. The server exposes NMDC's rich data resources through a standardized MCP interface, enabling AI assistants like Claude, ChatGPT, and others to search, query, and explore microbiology data.
The National Microbiology Data Center (国家微生物科学数据中心) is hosted by the Institute of Microbiology, Chinese Academy of Sciences. It provides comprehensive microbiology data services including:
Microbiome Data — BioProjects, BioSamples, Nucleotides, Metagenomes, Genomes, Proteins, SRA, and more
Microbial Resources — Global Catalogue of Microorganisms (GCM), biological parts
Virus Data — Virus pathogen sequences, SARS-CoV-2 genome and variation data
Pathogen Data — Pathogen catalogues, plasmids, phage, tuberculosis data
Fungi Data — Fungal names, genomes, type specimens
Microbial Dictionary — Biological terms, DNA barcodes
Microbial Catalog — Global microbial names, Chinese fungal specimens
The Model Context Protocol is an open standard for connecting AI applications to external systems. It provides a unified way for AI assistants to access data sources, tools, and workflows.
Related MCP server: datamgr
🔬 19 MCP Tools covering all major NMDC data categories
📚 5 MCP Resources for structured data access
🔄 Resource Templates for dynamic URI-based access
🌐 Async HTTP Client for efficient NMDC API communication
⚙️ Configurable via environment variables
📦 Easy Installation via pip or uv
# Using pip
pip install nmdc-mcp
# Or using uv
uv pip install nmdc-mcp
# Or from source
git clone https://github.com/zengzichao/NMDC-MCP.git
cd NMDC-MCP
pip install -e .Add the NMDC-MCP server to your MCP client configuration:
{
"mcpServers": {
"nmdc": {
"command": "nmdc-mcp",
"env": {
"NMDC_BASE_URL": "https://nmdc.cn"
}
}
}
}{
"mcp.servers": {
"nmdc": {
"command": "nmdc-mcp"
}
}
}Once configured, you can ask your AI assistant to interact with NMDC data:
Search NMDC for E. coli genome data
What analysis tools are available on NMDC?
Look up the BioProject PRJCA000001 on NMDC
Search the microbial dictionary for "bacteriophage"Tool | Description |
| Search across all NMDC databases by keyword |
| Get overview of all available data resources |
| Get BioProject details by accession ID |
| Get BioSample details by accession ID |
| Get sequence information by accession ID |
| Search genome records |
| Search Sequence Read Archive data |
| Search metagenome data |
| Search virus pathogen data |
| Search SARS-CoV-2 variation data |
| Search fungi microorganism data |
| Search pathogen microorganism data |
| Search tuberculosis data |
| Search Global Catalogue of Microorganisms |
| Search microbial dictionary for terms |
| Search microbial catalog |
| Get available analysis tools |
| Get metadata standards information |
| Get downloadable dataset list |
Environment Variable | Default | Description |
|
| NMDC website base URL |
|
| NMDC API base URL |
|
| HTTP request timeout (seconds) |
|
| Maximum results per query |
|
| Default page size for pagination |
git clone https://github.com/zengzichao/NMDC-MCP.git
cd NMDC-MCP
pip install -e ".[dev]"pytestruff check src/
mypy src/This project is licensed under the MIT License.
National Microbiology Data Center (NMDC) — for providing the data platform
Model Context Protocol — for the MCP specification
Institute of Microbiology, Chinese Academy of Sciences
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