Synapse.org
Search and metadata tools for Synapse scientific data
Discover and explore scientific datasets from collaborative research projects. Search Synapse for genomics, imaging, clinical data on cancer, neurodegenerative diseases, rare diseases, and more. Navigate project hierarchies and get detailed metadata and provenance to understand what datasets contain before you download.
When using an MCP server with Claude, please review Anthropic's data handling policies to understand how your data is processed:
You remain responsible for compliance with any data use restrictions and Synapse Terms of Service
Install
1Add the server to Claude Code
claude mcp add --transport http synapse-org https://mcp.synapse.org/mcp2Sign in
Run /mcp in Claude Code and complete the login flow for this server.
These instructions target Claude Code. Check the publisher's documentation for support in other Claude surfaces; a valid server URL alone does not establish compatibility.
JSON.mcp.json for a shared project
Commit this file so everyone on the project gets the same server.
{
"mcpServers": {
"synapse-org": {
"type": "http",
"url": "https://mcp.synapse.org/mcp"
}
}
}Tools
- get_entity
- get_entity_annotations
- get_entity_provenance
- get_entity_children
- search_synapse
About
Discover and explore scientific datasets from collaborative research projects. Search Synapse for genomics, imaging, clinical data on cancer, neurodegenerative diseases, rare diseases, and more. Navigate project hierarchies and get detailed metadata and provenance to understand what datasets contain before you download.
You can use the Synapse.org connector to:
Search for datasets and projects:
"Search Synapse for genomics datasets related to Alzheimer's disease"
Retrieve entity metadata:
"Get the metadata and provenance information for project syn12345678"
Traverse project hierarchies:
"Show me all the folders and files within the Cancer Research project"