Forge Tools lncipedia_lncrna

lncipedia_lncrna read

scidex.forge.lncipedia_lncrna

Query LNCipedia for human lncRNA gene and transcript records. Accepts a gene symbol (MALAT1), LNCipedia gene ID (lnc-MALAT1-1), or transcript ID (lnc-MALAT1-1:1). Returns genomic coordinates, transcript count, transcript lengths, exon counts, and aliases. Supports GRCh38 (default) and GRCh37 genome builds. Complements scidex.forge.lncbase (lncRNA-miRNA interactions) and scidex.forge.rnacentral (cross-database ncRNA IDs). LNCipedia is a comprehensive human lncRNA catalogue — free public API, no auth required.

HTTP: POST /api/scidex/forge/lncipedia_lncrna

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.lncipedia_lncrna``.",
  "properties": {
    "query": {
      "description": "Gene symbol (e.g. 'MALAT1'), LNCipedia gene ID (e.g. 'lnc-MALAT1-1'), or transcript ID (e.g. 'lnc-MALAT1-1:1') to look up.",
      "maxLength": 300,
      "minLength": 1,
      "title": "Query",
      "type": "string"
    },
    "build": {
      "default": "GRCh38",
      "description": "Genome assembly to anchor coordinates to. Default: 'GRCh38'.",
      "enum": [
        "GRCh38",
        "GRCh37"
      ],
      "title": "Build",
      "type": "string"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeLnciPediaIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "LnciPediaRecord": {
      "description": "One lncRNA gene record from LNCipedia.",
      "properties": {
        "gene_id": {
          "description": "LNCipedia gene ID (e.g. 'lnc-MALAT1-1').",
          "title": "Gene Id",
          "type": "string"
        },
        "gene_name": {
          "default": "",
          "description": "HGNC gene symbol (e.g. 'MALAT1').",
          "title": "Gene Name",
          "type": "string"
        },
        "aliases": {
          "description": "Alternative gene names and aliases.",
          "items": {
            "type": "string"
          },
          "title": "Aliases",
          "type": "array"
        },
        "chromosome": {
          "default": "",
          "description": "Chromosome (e.g. 'chr11').",
          "title": "Chromosome",
          "type": "string"
        },
        "start": {
          "default": 0,
          "description": "1-based genomic start coordinate.",
          "title": "Start",
          "type": "integer"
        },
        "end": {
          "default": 0,
          "description": "Genomic end coordinate.",
          "title": "End",
          "type": "integer"
        },
        "strand": {
          "default": "",
          "description": "Strand: '+' or '-'.",
          "title": "Strand",
          "type": "string"
        },
        "transcript_count": {
          "default": 0,
          "description": "Number of annotated transcripts.",
          "title": "Transcript Count",
          "type": "integer"
        },
        "transcripts": {
          "description": "Transcript records for this gene.",
          "items": {
            "$ref": "#/$defs/LnciPediaTranscript"
          },
          "title": "Transcripts",
          "type": "array"
        }
      },
      "required": [
        "gene_id"
      ],
      "title": "LnciPediaRecord",
      "type": "object"
    },
    "LnciPediaTranscript": {
      "description": "One transcript record from LNCipedia.",
      "properties": {
        "transcript_id": {
          "description": "LNCipedia transcript ID (e.g. 'lnc-MALAT1-1:1').",
          "title": "Transcript Id",
          "type": "string"
        },
        "length": {
          "default": 0,
          "description": "Transcript length in nucleotides.",
          "title": "Length",
          "type": "integer"
        },
        "exon_count": {
          "default": 0,
          "description": "Number of exons in this transcript.",
          "title": "Exon Count",
          "type": "integer"
        }
      },
      "required": [
        "transcript_id"
      ],
      "title": "LnciPediaTranscript",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.lncipedia_lncrna``.",
  "properties": {
    "query": {
      "description": "The query string that was submitted.",
      "title": "Query",
      "type": "string"
    },
    "records": {
      "description": "Matching lncRNA gene records from LNCipedia.",
      "items": {
        "$ref": "#/$defs/LnciPediaRecord"
      },
      "title": "Records",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when LNCipedia returned no records for the query.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "LNCipedia",
      "description": "Data source name.",
      "title": "Source",
      "type": "string"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeLnciPediaOut",
  "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/lncipedia_lncrna' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

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