Forge Tools lovd_variants

lovd_variants read

scidex.forge.lovd_variants

Look up unique genomic variant records from the LOVD3 shared database (Leiden Open Variation Database, databases.lovd.nl/shared) for a given gene symbol. Returns HGVS DNA/protein notation per transcript, genomic coordinates (hg19/hg38), LOVD DBID, times reported, and submitter info. LOVD is a gene-centered community variant database widely used in clinical genetics diagnostics. Distinct from forge_clinvar_variant (NCBI clinical significance), forge_gnomad_variant (population allele frequencies), and forge_civic_variants (cancer variant interpretations). API: databases.lovd.nl/shared/api/rest.php — public, no auth required.

HTTP: POST /api/scidex/forge/lovd_variants

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.lovd_variants``.",
  "properties": {
    "gene_symbol": {
      "description": "HGNC gene symbol (e.g. ``BRCA1``, ``CFTR``, ``DMD``). Case-sensitive — use official HGNC capitalization.",
      "maxLength": 64,
      "title": "Gene Symbol",
      "type": "string"
    },
    "build": {
      "default": "GRCh38",
      "description": "Reference genome build for genomic coordinates (default GRCh38).",
      "enum": [
        "GRCh38",
        "GRCh37"
      ],
      "title": "Build",
      "type": "string"
    },
    "limit": {
      "default": 50,
      "description": "Maximum number of unique variants to return (default 50, max 500).",
      "maximum": 500,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbol"
  ],
  "title": "ForgeLOVDVariantsIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "LOVDGenomicPosition": {
      "description": "Genomic position for a variant, keyed by reference build.",
      "properties": {
        "hg19": {
          "default": "",
          "description": "hg19/GRCh37 position (e.g. 'chr17:41197695').",
          "title": "Hg19",
          "type": "string"
        },
        "hg38": {
          "default": "",
          "description": "hg38/GRCh38 position (e.g. 'chr17:43045778').",
          "title": "Hg38",
          "type": "string"
        }
      },
      "title": "LOVDGenomicPosition",
      "type": "object"
    },
    "LOVDTranscriptVariant": {
      "description": "Variant annotation on one transcript.",
      "properties": {
        "transcript": {
          "description": "RefSeq transcript accession (e.g. 'NM_007294.3').",
          "title": "Transcript",
          "type": "string"
        },
        "dna": {
          "default": "",
          "description": "HGVS DNA notation (e.g. 'c.5266dupC').",
          "title": "Dna",
          "type": "string"
        },
        "rna": {
          "default": "",
          "description": "HGVS RNA notation (e.g. 'r.?).",
          "title": "Rna",
          "type": "string"
        },
        "protein": {
          "default": "",
          "description": "HGVS protein notation (e.g. 'p.(Gln1756Profs*74)').",
          "title": "Protein",
          "type": "string"
        }
      },
      "required": [
        "transcript"
      ],
      "title": "LOVDTranscriptVariant",
      "type": "object"
    },
    "LOVDVariant": {
      "description": "One unique variant record from LOVD shared.",
      "properties": {
        "dbid": {
          "default": "",
          "description": "LOVD DBID (e.g. 'BRCA1_001306').",
          "title": "Dbid",
          "type": "string"
        },
        "dna_notation": {
          "default": "",
          "description": "Primary HGVS DNA notation (e.g. 'NM_007294.3:c.5266dupC').",
          "title": "Dna Notation",
          "type": "string"
        },
        "genomic_position": {
          "$ref": "#/$defs/LOVDGenomicPosition",
          "description": "Genomic coordinates by build."
        },
        "genomic_notation": {
          "$ref": "#/$defs/LOVDGenomicPosition",
          "description": "HGVS genomic notation by build (e.g. 'chr17:g.43045778dup')."
        },
        "transcripts": {
          "description": "Per-transcript variant annotations.",
          "items": {
            "$ref": "#/$defs/LOVDTranscriptVariant"
          },
          "title": "Transcripts",
          "type": "array"
        },
        "times_reported": {
          "default": 0,
          "description": "Number of times this variant has been reported/submitted.",
          "minimum": 0,
          "title": "Times Reported",
          "type": "integer"
        },
        "owned_by": {
          "description": "Curators who own this variant entry.",
          "items": {
            "type": "string"
          },
          "title": "Owned By",
          "type": "array"
        },
        "created_date": {
          "default": "",
          "description": "ISO 8601 creation date.",
          "title": "Created Date",
          "type": "string"
        },
        "edited_date": {
          "default": "",
          "description": "ISO 8601 last edit date.",
          "title": "Edited Date",
          "type": "string"
        }
      },
      "title": "LOVDVariant",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.lovd_variants``.",
  "properties": {
    "gene_symbol": {
      "description": "The queried gene symbol.",
      "title": "Gene Symbol",
      "type": "string"
    },
    "variants": {
      "description": "Unique variant records from LOVD shared.",
      "items": {
        "$ref": "#/$defs/LOVDVariant"
      },
      "title": "Variants",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True if the gene symbol was not found in LOVD.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "LOVD3 Shared (databases.lovd.nl/shared)",
      "description": "Provenance of the variant data.",
      "title": "Source",
      "type": "string"
    },
    "took_ms": {
      "description": "Wall-clock time for the upstream API call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbol",
    "took_ms"
  ],
  "title": "ForgeLOVDVariantsOut",
  "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/lovd_variants' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbol": ""
}'

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