DROMA

Provides an MCP interface to load, normalize, analyze, and export DROMA cancer pharmacogenomics data via a stdio-based MCP server.

python

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GitHub Stars

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Language

3 months ago

First Indexed

3 weeks ago

Catalog Refreshed

Documentation & install

Readme and setup notes from the catalogue, plus a client-ready config you can copy for your MCP host.

Installation

Add the following to your MCP client configuration file.

Configuration

View docs

{
  "mcpServers": {
    "droma01-droma_mcp": {
      "command": "droma-mcp",
      "args": [
        "run",
        "--db-path",
        "path/to/droma.sqlite"
      ]
    }
  }
}

You can run and interact with the DROMA MCP Server to enable natural language exploration of drug-omics associations using a lightweight MCP client. This server loads DROMA datasets in memory, normalizes data on load, supports multiple projects, caches metadata for speed, and exports results for further analysis. It exposes a practical, flexible interface for AI-assisted pharmacogenomics workflows.

How to use

Start the MCP server in stdio mode to connect with AI assistants or local tools. Use the following command to launch the server with a local DROMA SQLite database path.

How to install

Prerequisites you need before installation:

Python 3.10+
R 4.0+ with DROMA.Set and DROMA.R packages
DROMA SQLite database
FastMCP 2.13+ (automatically installed)

How to use the server with an MCP client

Install the MCP package and then run the server in stdio mode. The server will be ready to accept commands from your MCP client for dataset management, data loading, analysis, and export.

Additional setup and configuration

Environment and runtime configuration helps you tailor the server to your environment. Ensure the DROMA SQLite database path is accessible and that your MCP client points to the correct startup command.

Available tools

load_dataset

Load DROMA datasets (CCLE, gCSI, etc.) into memory from the database.

list_loaded_datasets

Show which datasets are currently loaded in memory.

set_active_dataset

Set the active dataset for subsequent operations.

unload_dataset

Remove datasets from memory to free up resources.

load_molecular_profiles_normalized

Load molecular profiles (mRNA, CNV, methylation, etc.) with z-score normalization.

load_treatment_response_normalized

Load drug response data with normalization.

load_multi_project_molecular_profiles_normalized

Load data across multiple projects.

load_multi_project_treatment_response_normalized

Load treatment response across projects.

check_zscore_normalization

Verify normalization status of cached data.

get_cached_data_info

Get information about cached datasets.

export_cached_data

Export data to CSV/Excel/JSON formats.

get_droma_annotation

Retrieve sample or drug annotation data from the database.

list_droma_samples

List all available samples for a project with filtering options.

list_droma_features

List all available features (genes, drugs) for a project and data type.

list_droma_projects

List all projects available in the DROMA database.

plot_drug_sensitivity_rank

Create drug sensitivity rank plots.

analyze_drug_omic_pair

Analyze associations between drugs and omic features.