Forge Tools rfam_families

rfam_families read

scidex.forge.rfam_families

Query the Rfam database (rfam.org) for RNA family records by Rfam accession or keyword. Rfam is the authoritative database of non-coding RNA families including rRNA, snRNA, snoRNA, miRNA, tRNA, riboswitches, and more. Input: a Rfam accession (e.g. 'RF00001') for a direct lookup, or a keyword (e.g. 'snoRNA', '5S rRNA', 'riboswitch', 'tRNA') to search family descriptions. Returns family records with accession, identifier, RNA type, clan membership, seed/full sequence counts, average length, and consensus secondary structure. API: GET https://rfam.org/family/{rfam_acc} or /search/keyword/{keyword} — no authentication required.

HTTP: POST /api/scidex/forge/rfam_families

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.rfam_families``.",
  "properties": {
    "query": {
      "description": "Rfam accession (e.g. ``'RF00001'``) for a direct family lookup, or a keyword (e.g. ``'snoRNA'``, ``'5S rRNA'``, ``'riboswitch'``) to search across Rfam family descriptions and identifiers.",
      "maxLength": 200,
      "minLength": 1,
      "title": "Query",
      "type": "string"
    },
    "limit": {
      "default": 10,
      "description": "Maximum number of family records to return. Ignored for direct accession lookups (always returns 0 or 1). Default 10.",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeRfamFamiliesIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "RfamFamily": {
      "description": "One Rfam RNA family record.",
      "properties": {
        "rfam_acc": {
          "description": "Rfam accession (e.g. RF00001).",
          "title": "Rfam Acc",
          "type": "string"
        },
        "rfam_id": {
          "default": "",
          "description": "Short family identifier (e.g. 5S_rRNA).",
          "title": "Rfam Id",
          "type": "string"
        },
        "description": {
          "default": "",
          "description": "One-line human-readable description.",
          "title": "Description",
          "type": "string"
        },
        "rna_type": {
          "default": "",
          "description": "RNA type classification from Rfam (e.g. 'Gene; rRNA', 'Gene; snRNA; spliceosomal', 'Cis-reg; riboswitch').",
          "title": "Rna Type",
          "type": "string"
        },
        "clan_acc": {
          "default": "",
          "description": "Rfam clan accession (e.g. CL00113) if the family belongs to a clan.",
          "title": "Clan Acc",
          "type": "string"
        },
        "clan_id": {
          "default": "",
          "description": "Rfam clan identifier if available (e.g. RNaseP).",
          "title": "Clan Id",
          "type": "string"
        },
        "num_seed": {
          "default": 0,
          "description": "Number of sequences in the seed alignment.",
          "title": "Num Seed",
          "type": "integer"
        },
        "num_full": {
          "default": 0,
          "description": "Number of sequences in the full alignment (Rfam-annotated sequences).",
          "title": "Num Full",
          "type": "integer"
        },
        "average_length": {
          "default": 0,
          "description": "Average sequence length in nucleotides for the seed alignment.",
          "title": "Average Length",
          "type": "number"
        },
        "comment": {
          "default": "",
          "description": "Extended description or notes from Rfam curators.",
          "title": "Comment",
          "type": "string"
        },
        "ss_cons": {
          "default": "",
          "description": "Consensus secondary structure in dot-bracket notation (from seed alignment), if returned by the Rfam API.",
          "title": "Ss Cons",
          "type": "string"
        }
      },
      "required": [
        "rfam_acc"
      ],
      "title": "RfamFamily",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.rfam_families``.",
  "properties": {
    "query": {
      "description": "Echo of the input query string.",
      "title": "Query",
      "type": "string"
    },
    "families": {
      "description": "Rfam RNA family records matching the query.",
      "items": {
        "$ref": "#/$defs/RfamFamily"
      },
      "title": "Families",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when no matching families were found.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "Rfam (rfam.org)",
      "description": "Data source attribution.",
      "title": "Source",
      "type": "string"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for the upstream API call(s) in milliseconds.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeRfamFamiliesOut",
  "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/rfam_families' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

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