Forge Tools iedb_epitope

iedb_epitope read

scidex.forge.iedb_epitope

Query the Immune Epitope Database (IEDB) for experimentally validated T-cell and B-cell epitopes for a given antigen protein. Returns epitope sequences with MHC restriction (HLA alleles for T-cell), host organism, assay type, and immunogenicity outcome. Essential for vaccine design, immunotherapy hypothesis generation, and infectious disease research. Input: antigen (protein/molecule name), host_organism (default 'Homo sapiens'), epitope_type ('T cell', 'B cell', or 'both', default 'T cell'), limit. API: https://query-api.iedb.org — free, no auth required.

HTTP: POST /api/scidex/forge/iedb_epitope

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.iedb_epitope``.",
  "properties": {
    "antigen": {
      "description": "Antigen protein or source molecule name to query (e.g. 'spike protein', 'SARS-CoV-2', 'TP53').",
      "maxLength": 300,
      "title": "Antigen",
      "type": "string"
    },
    "host_organism": {
      "default": "Homo sapiens",
      "description": "Host organism in which epitope immunogenicity was tested. Pass an empty string to skip host-organism filtering. Default: 'Homo sapiens'.",
      "maxLength": 100,
      "title": "Host Organism",
      "type": "string"
    },
    "epitope_type": {
      "default": "T cell",
      "description": "Filter by immune cell type: 'T cell', 'B cell', or 'both' for all. Default: 'T cell'.",
      "enum": [
        "T cell",
        "B cell",
        "both"
      ],
      "title": "Epitope Type",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of epitope records to return (default 20, max 200).",
      "maximum": 200,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "antigen"
  ],
  "title": "ForgeIEDBEpitopeIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "IEDBEpitope": {
      "description": "One experimentally validated immune epitope from IEDB.",
      "properties": {
        "epitope_sequence": {
          "description": "Linear amino acid sequence of the epitope.",
          "title": "Epitope Sequence",
          "type": "string"
        },
        "epitope_type": {
          "description": "Immune cell type: 'T cell' or 'B cell'.",
          "title": "Epitope Type",
          "type": "string"
        },
        "mhc_allele": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "MHC restriction allele (e.g. HLA-A*02:01). None for B-cell epitopes.",
          "title": "Mhc Allele"
        },
        "host_organism": {
          "default": "",
          "description": "Host organism in which immunogenicity was tested (e.g. Homo sapiens).",
          "title": "Host Organism",
          "type": "string"
        },
        "assay_type": {
          "default": "",
          "description": "Experimental assay category (e.g. 'T cell assay', 'B cell assay').",
          "title": "Assay Type",
          "type": "string"
        },
        "qualitative_outcome": {
          "default": "",
          "description": "Immunogenicity result (e.g. 'Positive', 'Negative').",
          "title": "Qualitative Outcome",
          "type": "string"
        },
        "reference_count": {
          "default": 0,
          "description": "Number of PubMed references supporting this epitope.",
          "title": "Reference Count",
          "type": "integer"
        }
      },
      "required": [
        "epitope_sequence",
        "epitope_type"
      ],
      "title": "IEDBEpitope",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.iedb_epitope``.",
  "properties": {
    "antigen_name": {
      "description": "The antigen name as submitted.",
      "title": "Antigen Name",
      "type": "string"
    },
    "epitopes": {
      "description": "Experimentally validated immune epitope records.",
      "items": {
        "$ref": "#/$defs/IEDBEpitope"
      },
      "title": "Epitopes",
      "type": "array"
    },
    "total_found": {
      "default": 0,
      "description": "Total number of matching epitopes (may exceed the returned list).",
      "title": "Total Found",
      "type": "integer"
    },
    "not_found": {
      "default": false,
      "description": "True when IEDB returned no epitopes for the given antigen.",
      "title": "Not Found",
      "type": "boolean"
    }
  },
  "required": [
    "antigen_name"
  ],
  "title": "ForgeIEDBEpitopeOut",
  "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/iedb_epitope' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "antigen": ""
}'

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