Forge Tools collectri_regulons

collectri_regulons read

scidex.forge.collectri_regulons

Query CollecTRI for transcription factor (TF) regulons — the set of target genes regulated by a given TF, with signed mode-of-regulation (MOR) weights. CollecTRI is an expansion of DoRothEA; positive MOR = activation, negative MOR = repression. Ideal for decoupleR/VIPER TF-activity inference. Data is fetched from OmniPath (omnipathdb.org/interactions?datasets=collectri). Input: TF gene symbol, organism NCBI taxon ID (default 9606 = human), limit. Output: list of CollectriTarget(target_gene, effect, mor, evidence_sources), not_found flag, source attribution. No authentication required. Complements scidex.forge.dorothea_regulons (confidence A–E tiers), scidex.forge.jaspar_tfbs (binding motifs), scidex.forge.chea3 (inverse enrichment), and scidex.forge.omnipath_interactions (full network).

HTTP: POST /api/scidex/forge/collectri_regulons

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.collectri_regulons``.",
  "properties": {
    "tf_symbol": {
      "description": "HGNC gene symbol of the transcription factor to query (e.g. ``'TP53'``).",
      "title": "Tf Symbol",
      "type": "string"
    },
    "organism": {
      "default": "9606",
      "description": "NCBI taxonomy ID of the target organism. Default '9606' (Homo sapiens). Other common values: '10090' (Mus musculus), '10116' (Rattus norvegicus).",
      "title": "Organism",
      "type": "string"
    },
    "limit": {
      "default": 100,
      "description": "Maximum number of target records to return. Default 100.",
      "maximum": 500,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "tf_symbol"
  ],
  "title": "ForgeCollectriIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "CollectriTarget": {
      "description": "One CollecTRI TF–target gene interaction record.",
      "properties": {
        "target_gene": {
          "description": "HGNC symbol of the regulated target gene.",
          "title": "Target Gene",
          "type": "string"
        },
        "effect": {
          "description": "Direction of TF regulation derived from the mode-of-regulation (MOR) weight. 'positive' (activation) when mor > 0; 'negative' (repression) when mor < 0; 'unknown' when mor == 0 or absent.",
          "title": "Effect",
          "type": "string"
        },
        "mor": {
          "description": "Mode-of-regulation weight. Positive values indicate activation; negative values indicate repression. Magnitude reflects evidence strength.",
          "title": "Mor",
          "type": "number"
        },
        "evidence_sources": {
          "description": "Evidence databases supporting this TF–target interaction.",
          "items": {
            "type": "string"
          },
          "title": "Evidence Sources",
          "type": "array"
        }
      },
      "required": [
        "target_gene",
        "effect",
        "mor"
      ],
      "title": "CollectriTarget",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.collectri_regulons``.",
  "properties": {
    "tf_symbol": {
      "description": "TF gene symbol as queried.",
      "title": "Tf Symbol",
      "type": "string"
    },
    "targets": {
      "description": "Target genes regulated by this TF, sorted by absolute mor strength (strongest first), then alphabetically by target_gene. Empty when the TF has no regulon entries in CollecTRI.",
      "items": {
        "$ref": "#/$defs/CollectriTarget"
      },
      "title": "Targets",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when the TF is absent from CollecTRI entirely (the upstream API returned an empty result set for this TF).",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "OmniPath/CollecTRI",
      "description": "Data source attribution.",
      "title": "Source",
      "type": "string"
    }
  },
  "required": [
    "tf_symbol"
  ],
  "title": "ForgeCollectriOut",
  "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/collectri_regulons' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "tf_symbol": ""
}'

Discussion

Posting anonymously. Sign in for attribution.

No comments yet — be the first.