Forge Tools lncbase

lncbase read

scidex.forge.lncbase

Query DIANA-LncBase v3 for lncRNA-miRNA sponge (ceRNA) interactions. Returns experimentally validated and computationally predicted interactions between long non-coding RNAs and microRNAs, with interaction score, evidence type (experimental/predicted), tissue context, and PubMed references. Complements scidex.forge.mirbase_mirna (miRNA metadata) and scidex.forge.rnacentral (ncRNA IDs) with the ceRNA regulatory layer. Query by lncRNA symbol (e.g. MALAT1) or miRNA name (e.g. hsa-miR-21-5p). Filter by evidence_type ('experimental'/'predicted') and tissue. API: https://diana.e-ce.uth.gr/lncbasev3/api — free, no auth required.

HTTP: POST /api/scidex/forge/lncbase

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.lncbase``.",
  "properties": {
    "query": {
      "description": "Gene symbol, Ensembl ID (lncRNA mode), or mature miRNA name / MIMAT accession (mirna mode) to query. Examples: 'MALAT1', 'ENSG00000251562', 'hsa-miR-21-5p', 'MIMAT0000076'.",
      "maxLength": 300,
      "title": "Query",
      "type": "string"
    },
    "query_type": {
      "default": "lncrna",
      "description": "Whether to query by lncRNA ('lncrna') or miRNA ('mirna'). Default: 'lncrna'.",
      "enum": [
        "lncrna",
        "mirna"
      ],
      "title": "Query Type",
      "type": "string"
    },
    "tissue": {
      "anyOf": [
        {
          "maxLength": 200,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Optional tissue/cell type filter (case-insensitive substring match). Pass None to return all tissues.",
      "title": "Tissue"
    },
    "evidence_type": {
      "anyOf": [
        {
          "enum": [
            "experimental",
            "predicted"
          ],
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Filter by evidence type: 'experimental' for validated interactions, 'predicted' for computational predictions, or None for both. Default: None.",
      "title": "Evidence Type"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of interactions to return (default 20, max 200).",
      "maximum": 200,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeLncBaseIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "LncBaseInteraction": {
      "description": "One lncRNA-miRNA sponge interaction from DIANA-LncBase v3.",
      "properties": {
        "lncrna_id": {
          "description": "lncRNA gene identifier (e.g. ENSG00000251562).",
          "title": "Lncrna Id",
          "type": "string"
        },
        "lncrna_symbol": {
          "default": "",
          "description": "lncRNA gene symbol (e.g. MALAT1).",
          "title": "Lncrna Symbol",
          "type": "string"
        },
        "mirna_id": {
          "description": "miRNA identifier (e.g. MIMAT0000076).",
          "title": "Mirna Id",
          "type": "string"
        },
        "mirna_symbol": {
          "default": "",
          "description": "Mature miRNA name (e.g. hsa-miR-21-5p).",
          "title": "Mirna Symbol",
          "type": "string"
        },
        "interaction_score": {
          "description": "Confidence score in [0, 1]; higher means more confident.",
          "title": "Interaction Score",
          "type": "number"
        },
        "evidence_type": {
          "description": "Evidence type: 'experimental' or 'predicted'.",
          "title": "Evidence Type",
          "type": "string"
        },
        "tissue": {
          "description": "Tissue or cell types where the interaction is reported.",
          "items": {
            "type": "string"
          },
          "title": "Tissue",
          "type": "array"
        },
        "pmids": {
          "description": "PubMed IDs supporting this interaction.",
          "items": {
            "type": "string"
          },
          "title": "Pmids",
          "type": "array"
        }
      },
      "required": [
        "lncrna_id",
        "mirna_id",
        "interaction_score",
        "evidence_type"
      ],
      "title": "LncBaseInteraction",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.lncbase``.",
  "properties": {
    "interactions": {
      "description": "lncRNA-miRNA sponge interaction records from DIANA-LncBase v3.",
      "items": {
        "$ref": "#/$defs/LncBaseInteraction"
      },
      "title": "Interactions",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when LncBase returned no interactions for the given query.",
      "title": "Not Found",
      "type": "boolean"
    },
    "took_ms": {
      "description": "Wall-clock time for the upstream API call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "took_ms"
  ],
  "title": "ForgeLncBaseOut",
  "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/lncbase' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

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