Forge Tools mirtarbase

mirtarbase read

scidex.forge.mirtarbase

Query miRTarBase for experimentally validated miRNA–target gene interactions. Unlike sequence-based predictors, every interaction is supported by biological experiments (Luciferase reporter assays, Western blots, immunoprecipitation, etc.). Returns the validated target genes for a given miRNA, or the miRNAs that target a given gene, along with experimental evidence and PubMed reference counts. Complements scidex.forge.mirbase_mirna (sequences) with functional validation data. Input: query (miRNA ID or gene symbol), query_type ('mirna' or 'gene'), species filter (default 'Homo sapiens'), limit. API: https://mirtarbase.cuhk.edu.hk — free, no auth required.

HTTP: POST /api/scidex/forge/mirtarbase

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.mirtarbase``.",
  "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": "Whether to search by miRNA identifier ('mirna') or target gene symbol ('gene'). Default: 'mirna'.",
      "enum": [
        "mirna",
        "gene"
      ],
      "title": "Query Type",
      "type": "string"
    },
    "species": {
      "default": "Homo sapiens",
      "description": "Species filter applied client-side (case-insensitive substring match on the interaction's species field). Pass an empty string to skip filtering. Default: 'Homo sapiens'.",
      "maxLength": 100,
      "title": "Species",
      "type": "string"
    },
    "limit": {
      "default": 50,
      "description": "Maximum number of interaction records to return (default 50, max 500).",
      "maximum": 500,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeMiRTarBaseIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "MiRTarBaseInteraction": {
      "description": "One experimentally validated miRNA–target interaction from miRTarBase.",
      "properties": {
        "mirna_id": {
          "description": "Mature miRNA identifier (e.g. hsa-miR-21-5p).",
          "title": "Mirna Id",
          "type": "string"
        },
        "target_gene": {
          "description": "HGNC gene symbol of the validated target.",
          "title": "Target Gene",
          "type": "string"
        },
        "species": {
          "default": "",
          "description": "Organism in which the interaction was validated (e.g. Homo sapiens).",
          "title": "Species",
          "type": "string"
        },
        "experiments": {
          "description": "Experimental methods supporting this interaction (e.g. Luciferase reporter assay, Western blot).",
          "items": {
            "type": "string"
          },
          "title": "Experiments",
          "type": "array"
        },
        "support_type": {
          "default": "",
          "description": "Evidence class: 'Functional MTI' (target expression altered), 'Non-Functional MTI' (target bound but not altered), or 'Functional MTI (Weak)'.",
          "title": "Support Type",
          "type": "string"
        },
        "references_count": {
          "default": 0,
          "description": "Number of PubMed references supporting this interaction.",
          "title": "References Count",
          "type": "integer"
        }
      },
      "required": [
        "mirna_id",
        "target_gene"
      ],
      "title": "MiRTarBaseInteraction",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.mirtarbase``.",
  "properties": {
    "interactions": {
      "description": "Validated miRNA–target interaction records.",
      "items": {
        "$ref": "#/$defs/MiRTarBaseInteraction"
      },
      "title": "Interactions",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when miRTarBase returned no interactions for the query.",
      "title": "Not Found",
      "type": "boolean"
    }
  },
  "title": "ForgeMiRTarBaseOut",
  "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/mirtarbase' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

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