Forge Tools emdb_map

emdb_map read

scidex.forge.emdb_map

Fetch cryo-EM map metadata from the Electron Microscopy Data Bank (EMDB). Accepts either an EMDB accession (e.g. 'EMD-1234') for a direct entry lookup, or a free-text keyword to search EMDB. Returns map resolution, experimental method (single particle / tomography / helical), fitted PDB model IDs, map download URL, and viewer link. Source: EBI EMDB REST API (ebi.ac.uk/emdb/api) — public, no auth required.

HTTP: POST /api/scidex/forge/emdb_map

Invoke

Calls scidex.tool.invoke on the substrate with this tool name. Edit the JSON below — it must match the input schema. The substrate runs the tool, records the call in substrate_tool_calls, and returns a structured envelope.

Sign in to invoke this tool. Schema and curl snippet are visible to anyone.

Schemas

Input schema 
{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.emdb_map``.",
  "properties": {
    "emdb_id_or_query": {
      "description": "Either an EMDB accession (``'EMD-1234'`` or ``'emd-1234'``) for a direct single-entry lookup, or a free-text keyword/phrase (e.g. ``'spike protein cryo-em'``) to search EMDB.",
      "maxLength": 200,
      "minLength": 1,
      "title": "Emdb Id Or Query",
      "type": "string"
    },
    "rows": {
      "default": 10,
      "description": "Maximum number of search results to return when the input is treated as a free-text query. Ignored for direct EMD-ID lookups.",
      "maximum": 50,
      "minimum": 1,
      "title": "Rows",
      "type": "integer"
    }
  },
  "required": [
    "emdb_id_or_query"
  ],
  "title": "ForgeEmdbMapIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "EmdbMapEntry": {
      "description": "Metadata for one EMDB cryo-EM map entry.",
      "properties": {
        "emdb_id": {
          "description": "EMDB accession in canonical form, e.g. 'EMD-1234'.",
          "title": "Emdb Id",
          "type": "string"
        },
        "title": {
          "default": "",
          "description": "Entry title / sample description.",
          "title": "Title",
          "type": "string"
        },
        "resolution": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Resolution of the cryo-EM reconstruction in Ångströms, if reported.",
          "title": "Resolution"
        },
        "method": {
          "default": "",
          "description": "Experimental method: e.g. 'single particle', 'tomography', 'helical', 'subtomogram averaging'.",
          "title": "Method",
          "type": "string"
        },
        "fitted_pdbs": {
          "description": "PDB IDs of atomic models fitted into this map (from EMDB–PDB cross-references).",
          "items": {
            "type": "string"
          },
          "title": "Fitted Pdbs",
          "type": "array"
        },
        "map_url": {
          "default": "",
          "description": "Direct URL for the deposited map file (MRC/CCP4 format).",
          "title": "Map Url",
          "type": "string"
        },
        "viewer_url": {
          "default": "",
          "description": "EMDB web-viewer URL for human inspection.",
          "title": "Viewer Url",
          "type": "string"
        },
        "release_date": {
          "default": "",
          "description": "Public release date of the entry (ISO-8601 string when available).",
          "title": "Release Date",
          "type": "string"
        },
        "sample_name": {
          "default": "",
          "description": "Name of the biological sample or complex.",
          "title": "Sample Name",
          "type": "string"
        }
      },
      "required": [
        "emdb_id"
      ],
      "title": "EmdbMapEntry",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.emdb_map``.",
  "properties": {
    "query": {
      "description": "The input string as supplied.",
      "title": "Query",
      "type": "string"
    },
    "entries": {
      "description": "Matching EMDB map entries.",
      "items": {
        "$ref": "#/$defs/EmdbMapEntry"
      },
      "title": "Entries",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when a direct EMD-ID lookup returns no entry, or when a free-text search returns zero results.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "EMDB (ebi.ac.uk/emdb)",
      "description": "Data source attribution.",
      "title": "Source",
      "type": "string"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for the upstream API call(s) in milliseconds.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeEmdbMapOut",
  "type": "object"
}

curl snippet

Replace $SCIDEX_JWT with a valid bearer token. Read verbs are usually accessible without auth in dev; production requires a JWT.

curl -sS -X POST '/api/scidex/forge/emdb_map' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "emdb_id_or_query": ""
}'

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