Forge Tools mirdb_mirna_targets

mirdb_mirna_targets read

scidex.forge.mirdb_mirna_targets

Query miRDB v5.0 for machine-learning–predicted miRNA–target interactions. Returns computational predictions with target scores (0–100) across 5 species (Human, Mouse, Rat, Dog, Chicken). Distinct from scidex.forge.mirtarbase (experimentally validated): miRDB provides high-coverage predictions across 37k+ miRNAs with confidence scores. Input: query (miRNA ID or gene symbol), query_type ('mirna' or 'gene'), species (default 'Human'), min_target_score (default 50), limit (default 30). API: https://mirdb.org — free, no auth required.

HTTP: POST /api/scidex/forge/mirdb_mirna_targets

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.mirdb_mirna_targets``.",
  "properties": {
    "query": {
      "description": "miRNA identifier (e.g. ``hsa-miR-21-5p``) when query_type='mirna', or gene symbol (e.g. ``TP53``) when query_type='gene'.",
      "maxLength": 200,
      "title": "Query",
      "type": "string"
    },
    "query_type": {
      "default": "mirna",
      "description": "Search by miRNA identifier ('mirna') or gene symbol ('gene'). Default: 'mirna'.",
      "enum": [
        "mirna",
        "gene"
      ],
      "title": "Query Type",
      "type": "string"
    },
    "species": {
      "default": "Human",
      "description": "Species for the search. One of: Human, Mouse, Rat, Dog, Chicken. Default: Human.",
      "enum": [
        "Human",
        "Mouse",
        "Rat",
        "Dog",
        "Chicken"
      ],
      "title": "Species",
      "type": "string"
    },
    "min_target_score": {
      "default": 50,
      "description": "Minimum target score threshold (0–100). Default: 50.",
      "maximum": 100,
      "minimum": 0,
      "title": "Min Target Score",
      "type": "integer"
    },
    "limit": {
      "default": 30,
      "description": "Maximum number of target records to return (default 30, max 200).",
      "maximum": 200,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeMirdbIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "MirdbTarget": {
      "description": "One miRDB computational miRNA–target prediction.",
      "properties": {
        "mirna_id": {
          "description": "Mature miRNA identifier (e.g. hsa-miR-21-5p).",
          "title": "Mirna Id",
          "type": "string"
        },
        "target_gene": {
          "description": "Gene symbol of the predicted target.",
          "title": "Target Gene",
          "type": "string"
        },
        "target_score": {
          "description": "miRDB target score 0–100; higher = more confident prediction. Scores ≥ 80 are considered high-confidence.",
          "maximum": 100,
          "minimum": 0,
          "title": "Target Score",
          "type": "integer"
        }
      },
      "required": [
        "mirna_id",
        "target_gene",
        "target_score"
      ],
      "title": "MirdbTarget",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.mirdb_mirna_targets``.",
  "properties": {
    "targets": {
      "description": "Predicted miRNA–target records, sorted by target_score descending.",
      "items": {
        "$ref": "#/$defs/MirdbTarget"
      },
      "title": "Targets",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when miRDB returned no predictions for the query.",
      "title": "Not Found",
      "type": "boolean"
    }
  },
  "title": "ForgeMirdbOut",
  "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/mirdb_mirna_targets' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

Discussion

Posting anonymously. Sign in for attribution.

No comments yet — be the first.