Forge Tools mirbase_mirna

mirbase_mirna read

scidex.forge.mirbase_mirna

Look up microRNA annotations from miRBase, the primary repository for miRNA genes. Returns mature miRNA identifiers, MIMAT accessions, nucleotide sequences, chromosomal locations, stem-loop (precursor) accessions, and target gene symbols. miRNAs regulate gene expression post-transcriptionally and are critical in cancer, development, and disease research. Query by mature miRNA ID (e.g. hsa-miR-21-5p) or gene/locus symbol (e.g. MIR21). Species filter defaults to hsa (Homo sapiens). REST API: https://mirbase.org/webapi — free, no auth required.

HTTP: POST /api/scidex/forge/mirbase_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.mirbase_mirna``.",
  "properties": {
    "mirna_id": {
      "default": "",
      "description": "Mature miRNA identifier to search (e.g. ``hsa-miR-21-5p``, ``hsa-miR-21``, ``MIMAT0000076``). At least one of mirna_id or gene_symbol is required.",
      "maxLength": 200,
      "title": "Mirna Id",
      "type": "string"
    },
    "gene_symbol": {
      "default": "",
      "description": "Gene/locus symbol associated with the miRNA (e.g. ``MIR21``). At least one of mirna_id or gene_symbol is required.",
      "maxLength": 200,
      "title": "Gene Symbol",
      "type": "string"
    },
    "species": {
      "default": "hsa",
      "description": "Species prefix to filter results (e.g. ``hsa`` for Homo sapiens, ``mmu`` for Mus musculus, ``rno`` for Rattus norvegicus). Results whose miRNA name does not start with this prefix are excluded.",
      "maxLength": 20,
      "title": "Species",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of miRNA records to return (default 20, max 100).",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "title": "ForgeMiRBaseIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "MiRNAEntry": {
      "description": "One miRBase mature miRNA annotation record.",
      "properties": {
        "mirna_id": {
          "description": "Mature miRNA identifier (e.g. hsa-miR-21-5p).",
          "title": "Mirna Id",
          "type": "string"
        },
        "mirna_accession": {
          "default": "",
          "description": "MIMAT accession (e.g. MIMAT0000076).",
          "title": "Mirna Accession",
          "type": "string"
        },
        "mirna_name": {
          "default": "",
          "description": "miRNA name (typically same as mirna_id).",
          "title": "Mirna Name",
          "type": "string"
        },
        "species": {
          "default": "",
          "description": "Species prefix extracted from the miRNA name (e.g. hsa).",
          "title": "Species",
          "type": "string"
        },
        "sequence": {
          "default": "",
          "description": "Mature miRNA nucleotide sequence (U-alphabet).",
          "title": "Sequence",
          "type": "string"
        },
        "target_genes": {
          "description": "Predicted/validated target gene symbols from the miRBase target endpoint.",
          "items": {
            "type": "string"
          },
          "title": "Target Genes",
          "type": "array"
        },
        "chromosomal_location": {
          "default": "",
          "description": "Genomic location of the precursor locus (e.g. chr17:57918627-57918698).",
          "title": "Chromosomal Location",
          "type": "string"
        },
        "stem_loop_accession": {
          "default": "",
          "description": "Precursor/stem-loop MI accession (e.g. MI0000077).",
          "title": "Stem Loop Accession",
          "type": "string"
        }
      },
      "required": [
        "mirna_id"
      ],
      "title": "MiRNAEntry",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.mirbase_mirna``.",
  "properties": {
    "mirnas": {
      "description": "miRBase mature miRNA annotation records.",
      "items": {
        "$ref": "#/$defs/MiRNAEntry"
      },
      "title": "Mirnas",
      "type": "array"
    },
    "total_found": {
      "default": 0,
      "description": "Total results returned by miRBase before the limit was applied.",
      "title": "Total Found",
      "type": "integer"
    },
    "took_ms": {
      "description": "Wall-clock time for the upstream API calls.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "took_ms"
  ],
  "title": "ForgeMiRBaseOut",
  "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/mirbase_mirna' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{}'

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