Forge Tools targetscan_mirna

targetscan_mirna read

scidex.forge.targetscan_mirna

Query TargetScan (targetscan.org) for computationally predicted miRNA target sites using seed complementarity and context++ scores. TargetScan is the canonical source for 3' UTR miRNA target predictions, distinct from miRDB (Miranda algorithm) and miRTarBase (experimentally validated). Returns target gene symbol, miRNA family, site type (8mer/7mer-m8/7mer-1a), context++ score, weighted context++ score, conservation score, and UTR coordinate. Input: query (gene symbol or miRNA family ID), query_type ('gene' or 'mirna'), species_tax_id (default 9606 for human), genus ('vert'), limit (default 20, max 20). API: https://www.targetscan.org — free, no auth required.

HTTP: POST /api/scidex/forge/targetscan_mirna

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.targetscan_mirna``.",
  "properties": {
    "query": {
      "description": "Gene symbol (e.g. 'TP53') when query_type='gene', or miRNA family ID (e.g. 'hsa-miR-21') when query_type='mirna'.",
      "maxLength": 100,
      "title": "Query",
      "type": "string"
    },
    "query_type": {
      "default": "gene",
      "description": "Search by target gene symbol ('gene') or miRNA family ID ('mirna'). Default: 'gene'.",
      "enum": [
        "gene",
        "mirna"
      ],
      "title": "Query Type",
      "type": "string"
    },
    "species_tax_id": {
      "default": 9606,
      "description": "NCBI TaxID of the species. Default: 9606 (human).",
      "title": "Species Tax Id",
      "type": "integer"
    },
    "genus": {
      "default": "vert",
      "description": "TargetScan genus group. Use 'vert' for vertebrate queries. Default: 'vert'.",
      "enum": [
        "vertebrate",
        "vert"
      ],
      "title": "Genus",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of predictions to return (default 20, max 20).",
      "maximum": 20,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeTargetscanIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "TargetScanPrediction": {
      "description": "One TargetScan computational miRNA–target site prediction.",
      "properties": {
        "target_gene_symbol": {
          "description": "HGNC gene symbol of the predicted miRNA target.",
          "title": "Target Gene Symbol",
          "type": "string"
        },
        "mirna_family": {
          "description": "TargetScan miRNA family ID (e.g. 'hsa-miR-21-5p/21-3p' family). Use this rather than a specific mature miRNA when querying by gene.",
          "title": "Mirna Family",
          "type": "string"
        },
        "site_type": {
          "description": "Seed match site type: '8mer' (7mer-A1 + m8), '7mer-m8' (7mer-m8), or '7mer-1a' (7mer-1A). 8mer sites have the highest predicted efficacy.",
          "enum": [
            "8mer",
            "7mer-m8",
            "7mer-1a"
          ],
          "title": "Site Type",
          "type": "string"
        },
        "context_plus_plus_score": {
          "description": "context++ score for this specific site. Lower (more negative) = stronger predicted repression. Not directly comparable across genes.",
          "title": "Context Plus Plus Score",
          "type": "number"
        },
        "weighted_context_score": {
          "description": "Weighted context++ score normalised by UTR length and site number. Lower (more negative) = more reliably repressed.",
          "title": "Weighted Context Score",
          "type": "number"
        },
        "conservation_score": {
          "description": "Aggregate conservation score of the aligned site across species. Higher = more conserved. Values typically range 0–1.",
          "title": "Conservation Score",
          "type": "number"
        },
        "utr_coordinate": {
          "description": "1-based position of the site start in the target gene's 3' UTR.",
          "minimum": 1,
          "title": "Utr Coordinate",
          "type": "integer"
        }
      },
      "required": [
        "target_gene_symbol",
        "mirna_family",
        "site_type",
        "context_plus_plus_score",
        "weighted_context_score",
        "conservation_score",
        "utr_coordinate"
      ],
      "title": "TargetScanPrediction",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.targetscan_mirna``.",
  "properties": {
    "predictions": {
      "description": "Predicted miRNA target sites, sorted by context++ score ascending.",
      "items": {
        "$ref": "#/$defs/TargetScanPrediction"
      },
      "title": "Predictions",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when TargetScan returned no predictions for the query.",
      "title": "Not Found",
      "type": "boolean"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for upstream API calls in milliseconds.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "title": "ForgeTargetscanOut",
  "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/targetscan_mirna' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

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