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Synapse MCP connector

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Connect to the Synapse MCP server (Sage Bionetworks) to explore Synapse entities, annotations, provenance, and project structure, and to search...

Synapse MCP connector

  1. Terminal window
    npm install @scalekit-sdk/node

    Full SDK reference: Node.js | Python

  2. Add your Scalekit credentials to your .env file. Find values in app.scalekit.com > Developers > API Credentials.

    .env
    SCALEKIT_ENVIRONMENT_URL=<your-environment-url>
    SCALEKIT_CLIENT_ID=<your-client-id>
    SCALEKIT_CLIENT_SECRET=<your-client-secret>
  3. quickstart.ts
    import { ScalekitClient } from '@scalekit-sdk/node'
    import 'dotenv/config'
    const scalekit = new ScalekitClient(
    process.env.SCALEKIT_ENV_URL,
    process.env.SCALEKIT_CLIENT_ID,
    process.env.SCALEKIT_CLIENT_SECRET,
    )
    const actions = scalekit.actions
    const connector = 'synapsemcp'
    const identifier = 'user_123'
    // Generate an authorization link for the user
    const { link } = await actions.getAuthorizationLink({ connectionName: connector, identifier })
    console.log('Authorize Synapse MCP:', link)
    process.stdout.write('Press Enter after authorizing...')
    await new Promise(r => process.stdin.once('data', r))
    // Make your first call
    const result = await actions.executeTool({
    connector,
    identifier,
    toolName: 'synapsemcp_search_synapse',
    toolInput: {},
    })
    console.log(result)

Connect this agent connector to let your agent:

  • Search synapse — Search Synapse entities using keyword queries with optional name/type/parent filters
  • Get entity provenance, entity children, entity annotations — Return provenance (activity) metadata for a Synapse entity, including inputs and code executed

Use the exact tool names from the Tool list below when you call execute_tool. If you’re not sure which name to use, list the tools available for the current user first.

synapsemcp_get_entity#Return Synapse entity metadata by ID (projects, folders, files, tables, etc.). Only retrieves metadata information - does not download file content.1 param

Return Synapse entity metadata by ID (projects, folders, files, tables, etc.). Only retrieves metadata information - does not download file content.

NameTypeRequiredDescription
entity_idstringrequiredThe Synapse entity ID to fetch (for example syn123456).
synapsemcp_get_entity_annotations#Return custom annotation key/value pairs for a Synapse entity.1 param

Return custom annotation key/value pairs for a Synapse entity.

NameTypeRequiredDescription
entity_idstringrequiredThe Synapse entity ID whose annotations to fetch (for example syn123456).
synapsemcp_get_entity_children#List children for Synapse container entities (projects or folders).1 param

List children for Synapse container entities (projects or folders).

NameTypeRequiredDescription
entity_idstringrequiredThe Synapse container entity ID (project or folder) whose children to list (for example syn123456).
synapsemcp_get_entity_provenance#Return provenance (activity) metadata for a Synapse entity, including inputs and code executed.2 params

Return provenance (activity) metadata for a Synapse entity, including inputs and code executed.

NameTypeRequiredDescription
entity_idstringrequiredThe Synapse entity ID whose provenance to fetch (for example syn123456).
versionintegeroptionalOptional entity version number to scope the provenance to a specific version. Omit for the latest version.
synapsemcp_search_synapse#Search Synapse entities using keyword queries with optional name/type/parent filters. Results are served by Synapse as data custodian. Attribution and licensing are determined by the original contributors; check the specific entity's annotations or Wiki for details.7 params

Search Synapse entities using keyword queries with optional name/type/parent filters. Results are served by Synapse as data custodian. Attribution and licensing are determined by the original contributors; check the specific entity's annotations or Wiki for details.

NameTypeRequiredDescription
entity_typestringoptionalFilter results to a single entity type (for example file, folder, project, table).
entity_typesarrayoptionalFilter results to multiple entity types. Pass as a JSON array of strings via the SDK, not as a string.
limitintegeroptionalMaximum number of results to return.
namestringoptionalFilter results to entities matching this exact name.
offsetintegeroptionalNumber of results to skip, for pagination.
parent_idstringoptionalRestrict the search to entities under this parent container ID (for example syn123456).
query_termstringoptionalFree-text keyword query to search Synapse entities.