Forge Tools rnacentral

rnacentral read

scidex.forge.rnacentral

Look up non-coding RNA entries from RNAcentral, the central repository integrating 50+ databases (GENCODE, Ensembl, RefSeq, miRBase, Rfam, …) for ncRNA sequences. Returns URS identifiers, RNA class (lncRNA, snoRNA, snRNA, piRNA, tRNA, rRNA, miRNA), sequence length, species, contributing databases, gene symbols, and cross-reference IDs. Query by gene name (HOTAIR, MALAT1, SNORD) or description keyword. Species defaults to human (NCBI taxid 9606). Optional rna_type filter narrows results to a specific RNA class. REST API: https://rnacentral.org/api/v1/ — free, no auth required.

HTTP: POST /api/scidex/forge/rnacentral

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.rnacentral``.",
  "properties": {
    "query": {
      "description": "Search term for non-coding RNA entries (e.g. gene name ``HOTAIR``, ``MALAT1``, ``SNORD``, or functional annotation keyword).",
      "maxLength": 500,
      "title": "Query",
      "type": "string"
    },
    "rna_type": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Optional RNA class filter (e.g. ``lncRNA``, ``snoRNA``, ``snRNA``, ``piRNA``, ``tRNA``, ``rRNA``, ``miRNA``). Case-insensitive substring match.",
      "title": "Rna Type"
    },
    "species": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": "human",
      "description": "Species common name or scientific name to restrict results (e.g. ``human``, ``mouse``, ``zebrafish``). Defaults to ``human`` (NCBI taxid 9606). Pass ``None`` to search across all species.",
      "title": "Species"
    },
    "limit": {
      "default": 10,
      "description": "Maximum number of RNA records to return (default 10, max 50).",
      "maximum": 50,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeRNACentralIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "RNACentralEntry": {
      "description": "One RNAcentral non-coding RNA entry.",
      "properties": {
        "upi": {
          "description": "RNAcentral URS identifier (e.g. URS0000000001).",
          "title": "Upi",
          "type": "string"
        },
        "description": {
          "default": "",
          "description": "Human-readable description from member databases.",
          "title": "Description",
          "type": "string"
        },
        "rna_type": {
          "default": "",
          "description": "RNA class (e.g. lncRNA, snoRNA, tRNA, miRNA).",
          "title": "Rna Type",
          "type": "string"
        },
        "length": {
          "default": 0,
          "description": "Sequence length in nucleotides.",
          "title": "Length",
          "type": "integer"
        },
        "species": {
          "default": "",
          "description": "Scientific species name (e.g. Homo sapiens).",
          "title": "Species",
          "type": "string"
        },
        "taxon_id": {
          "default": 0,
          "description": "NCBI taxonomy identifier.",
          "title": "Taxon Id",
          "type": "integer"
        },
        "databases": {
          "description": "Member databases that contain this sequence.",
          "items": {
            "type": "string"
          },
          "title": "Databases",
          "type": "array"
        },
        "gene_name": {
          "default": "",
          "description": "Gene symbol if available.",
          "title": "Gene Name",
          "type": "string"
        },
        "external_ids": {
          "description": "Cross-reference accession identifiers from member databases.",
          "items": {
            "type": "string"
          },
          "title": "External Ids",
          "type": "array"
        }
      },
      "required": [
        "upi"
      ],
      "title": "RNACentralEntry",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.rnacentral``.",
  "properties": {
    "query": {
      "description": "The search query submitted.",
      "title": "Query",
      "type": "string"
    },
    "rna_type_filter": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "RNA type filter applied to results, if any.",
      "title": "Rna Type Filter"
    },
    "results": {
      "description": "Non-coding RNA entries from RNAcentral.",
      "items": {
        "$ref": "#/$defs/RNACentralEntry"
      },
      "title": "Results",
      "type": "array"
    },
    "total_found": {
      "default": 0,
      "description": "Total results reported by RNAcentral before the limit was applied.",
      "title": "Total Found",
      "type": "integer"
    },
    "not_found": {
      "default": false,
      "description": "True if no results matched the query.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "RNAcentral",
      "description": "Data source identifier.",
      "title": "Source",
      "type": "string"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeRNACentralOut",
  "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/rnacentral' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

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