Forge Tools corum_complexes

corum_complexes read

scidex.forge.corum_complexes

Look up protein complex membership from CORUM (Comprehensive Resource of Mammalian protein complexes) via the OmniPath REST API. CORUM contains 4,274 manually annotated mammalian protein complexes — the gold standard for complex-level analysis. For each input gene symbol, returns complexes that include it as a subunit, with complex name, subunit list, source databases, and GO terms. Complements pairwise interaction data from forge_intact_interactions and forge_string_ppi. REST API: https://omnipathdb.org/complexes — free, no auth.

HTTP: POST /api/scidex/forge/corum_complexes

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.corum_complexes``.",
  "properties": {
    "gene_symbols": {
      "description": "Gene symbols to query (e.g. ``['BRCA1', 'TP53']``). OmniPath returns complexes containing at least one of these genes. 1–10 symbols per call.",
      "items": {
        "type": "string"
      },
      "maxItems": 10,
      "minItems": 1,
      "title": "Gene Symbols",
      "type": "array"
    },
    "species": {
      "default": "Homo sapiens",
      "description": "Species to filter complexes by. Defaults to 'Homo sapiens'. Common alternatives: 'Mus musculus', 'Rattus norvegicus'.",
      "maxLength": 100,
      "title": "Species",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of complexes to return. Default 20.",
      "maximum": 200,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbols"
  ],
  "title": "ForgeCORUMIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "CORUMComplex": {
      "description": "One CORUM protein complex entry.",
      "properties": {
        "complex_id": {
          "default": "",
          "description": "CORUM complex identifier (e.g. 'CORUM:7'). Empty when not in CORUM.",
          "title": "Complex Id",
          "type": "string"
        },
        "complex_name": {
          "description": "Human-readable complex name.",
          "title": "Complex Name",
          "type": "string"
        },
        "subunits": {
          "description": "Gene symbols of subunit proteins in this complex.",
          "items": {
            "type": "string"
          },
          "title": "Subunits",
          "type": "array"
        },
        "subunit_count": {
          "default": 0,
          "description": "Total number of unique subunits in the complex.",
          "title": "Subunit Count",
          "type": "integer"
        },
        "sources": {
          "description": "Source database names (e.g. ['CORUM', 'ComplexPortal']).",
          "items": {
            "type": "string"
          },
          "title": "Sources",
          "type": "array"
        },
        "go_terms": {
          "description": "GO term identifiers annotated to this complex.",
          "items": {
            "type": "string"
          },
          "title": "Go Terms",
          "type": "array"
        },
        "disease_associations": {
          "description": "Disease names or identifiers associated with this complex.",
          "items": {
            "type": "string"
          },
          "title": "Disease Associations",
          "type": "array"
        }
      },
      "required": [
        "complex_name"
      ],
      "title": "CORUMComplex",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.corum_complexes``.",
  "properties": {
    "gene_symbols": {
      "description": "The gene symbols that were queried.",
      "items": {
        "type": "string"
      },
      "title": "Gene Symbols",
      "type": "array"
    },
    "complexes": {
      "description": "CORUM complex records. Empty when no complex contains the queried genes.",
      "items": {
        "$ref": "#/$defs/CORUMComplex"
      },
      "title": "Complexes",
      "type": "array"
    },
    "total_found": {
      "description": "Total unique complexes found before limit was applied.",
      "title": "Total Found",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbols",
    "total_found"
  ],
  "title": "ForgeCORUMOut",
  "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/corum_complexes' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbols": []
}'

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