EMDB Entry Metadata (Cryo-EM Map Record by Accession ID)

emdb/entry

Returns the full Electron Microscopy Data Bank record for one entry id such as EMD-1832: title, authors, keywords, release status and key dates, the primary citation, the map file's name, format, grid dimensions, cell and statistics, figure files, and the macromolecules in the sample. The map volume itself is not returned, only its description. An unknown id fails. Data from the EMDB, passed through unmodified and served by Omnial; not an official EMDB product.

activeper callv1

Price

$0.0026 per call

You pay the price shown. If a call turns out to cost more than its quote, you pay the actual price, capped at twice the quote. No monthly minimum. Top-ups start at $5.

Data source

Electron Microscopy Data Bank (EMDB)

Data from the Electron Microscopy Data Bank (EMDB), EMBL-EBI, with no copyright restrictions per ebi.ac.uk/emdb/documentation/faq. Credit the original authors of the structure data and the EMDB accession id. Served by Eden Engine; not an official EMDB product.

Use it

Five steps: search, inspect, learn, run, settle. No per-tool setup; your agent reaches this tool through the meta-tools it already has.

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agent

// 1. search: find the tool
omnial_search({ query: "what you need" })

// 2. inspect: price and input schema
omnial_inspect({ tool: "emdb/entry" })

// 3. learn: read the usage guide at runtime
omnial_learn({ tool: "emdb/entry" })

// 4. run: price the exact call first, then run it
omnial_execute({ tool: "emdb/entry", input: { /* see input_schema */ }, dry_run: true })
omnial_execute({ tool: "emdb/entry", input: { /* ... */ } })

// 5. settle: the call is charged when it finishes, nothing to do

Not connected yet? Point your MCP client at https://mcp.eden-engine.com/mcp, then copy a config for your client.

Pricing

Every charge this tool can incur.

Charge	Price
Per call	$0.0026

Updated: Oct 20, 2026

Input and output schemas

Input schema

input_schema.json

{
  "type": "object",
  "required": [
    "emdb_id"
  ],
  "properties": {
    "emdb_id": {
      "type": "string",
      "pattern": "^EMD-[0-9]{1,8}$",
      "description": "The EMDB accession id: EMD- followed by digits, for example EMD-1832 or EMD-74682."
    }
  },
  "additionalProperties": false
}

Output schema

output_schema.json

{
  "type": "object",
  "required": [
    "emdb_id",
    "admin"
  ],
  "properties": {
    "_id": {
      "type": "string",
      "description": "The archive's internal record id."
    },
    "map": {
      "type": "object",
      "description": "The map file's description: `file`, `format`, `data_type`, `dimensions`, `cell`, `pixel_spacing`, `size_kbytes`, `statistics` and `contour_list`. Values with units are objects with `units` and `valueOf_`.",
      "additionalProperties": true
    },
    "admin": {
      "type": "object",
      "description": "Administrative data: `title`, `keywords`, `authors_list`, `current_status`, `key_dates` (deposition, header release, map release, update) and the processing sites.",
      "additionalProperties": true
    },
    "sample": {
      "type": "object",
      "description": "What was imaged, including the macromolecule list.",
      "additionalProperties": true
    },
    "emdb_id": {
      "type": "string",
      "description": "The EMDB accession id, for example EMD-1832."
    },
    "interpretation": {
      "type": "object",
      "description": "Figure files for the entry.",
      "additionalProperties": true
    },
    "crossreferences": {
      "type": "object",
      "description": "Links to other records, including the primary citation (authors, journal, year, title, PubMed and DOI references where published).",
      "additionalProperties": true
    }
  },
  "description": "The EMDB entry record as the archive serves it.",
  "additionalProperties": true
}