Forge Tools trrust_regulation

trrust_regulation read

scidex.forge.trrust_regulation

Query TRRUST v2 for transcription factor (TF) regulatory relationships. TRRUST is a curated database of human TF→target interactions with mode (Activation / Repression / Unknown) and PubMed support. Input: gene symbol (HGNC), role ('tf' | 'target' | 'both', default 'both'), limit (default 50). Output: list of Interaction(tf, target, mode, pmids), not_found flag. Source: https://www.grnpedia.org/trrust/ — public, no auth required. Complements scidex.forge.dorothea_regulons (confidence-graded TF regulons) and scidex.forge.omnipath_interactions (broad signaling network).

HTTP: POST /api/scidex/forge/trrust_regulation

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.trrust_regulation``.",
  "properties": {
    "tf_or_target": {
      "description": "HGNC gene symbol to look up in TRRUST. Use ``role`` to control whether this is matched as a TF, a target gene, or either.",
      "maxLength": 30,
      "minLength": 1,
      "title": "Tf Or Target",
      "type": "string"
    },
    "role": {
      "default": "both",
      "description": "Which side of the regulatory relationship to match: 'tf' = transcription factor only, 'target' = regulated target gene only, 'both' = either TF or target (default).",
      "enum": [
        "tf",
        "target",
        "both"
      ],
      "title": "Role",
      "type": "string"
    },
    "limit": {
      "default": 50,
      "description": "Maximum number of regulatory relationships to return. Default 50.",
      "maximum": 500,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "tf_or_target"
  ],
  "title": "ForgeTRRUSTIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "Interaction": {
      "description": "One TRRUST TF→target regulatory relationship.",
      "properties": {
        "tf": {
          "description": "HGNC gene symbol of the transcription factor.",
          "title": "Tf",
          "type": "string"
        },
        "target": {
          "description": "HGNC gene symbol of the regulated target gene.",
          "title": "Target",
          "type": "string"
        },
        "mode": {
          "description": "Direction of regulation: 'Activation', 'Repression', or 'Unknown'.",
          "enum": [
            "Activation",
            "Repression",
            "Unknown"
          ],
          "title": "Mode",
          "type": "string"
        },
        "pmids": {
          "description": "PubMed IDs supporting this regulatory relationship.",
          "items": {
            "type": "string"
          },
          "title": "Pmids",
          "type": "array"
        }
      },
      "required": [
        "tf",
        "target",
        "mode"
      ],
      "title": "Interaction",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.trrust_regulation``.",
  "properties": {
    "query": {
      "description": "Queried gene symbol (as supplied).",
      "title": "Query",
      "type": "string"
    },
    "role": {
      "description": "Role filter used for this query.",
      "enum": [
        "tf",
        "target",
        "both"
      ],
      "title": "Role",
      "type": "string"
    },
    "interactions": {
      "description": "TF→target regulatory relationships matching the query. Sorted alphabetically by TF, then by target gene.",
      "items": {
        "$ref": "#/$defs/Interaction"
      },
      "title": "Interactions",
      "type": "array"
    },
    "returned": {
      "description": "Length of ``interactions``.",
      "title": "Returned",
      "type": "integer"
    },
    "not_found": {
      "default": false,
      "description": "True when the queried gene symbol does not appear in TRRUST in any regulatory relationship for the specified role.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "TRRUST v2 (grnpedia.org)",
      "description": "Data source: 'TRRUST v2 (grnpedia.org)'.",
      "title": "Source",
      "type": "string"
    }
  },
  "required": [
    "query",
    "role",
    "returned"
  ],
  "title": "ForgeTRRUSTOut",
  "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/trrust_regulation' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "tf_or_target": ""
}'

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