Lovd Tools#

Configuration File: lovd_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the lovd_tools.json configuration file.

Available Tools#

LOVD_get_gene (Type: LOVDTool)#

Get a complete LOVD gene record after normalizing the HGNC symbol to uppercase and verifying the …

LOVD_get_gene tool specification

Tool Information:

  • Name: LOVD_get_gene

  • Type: LOVDTool

  • Description: Get a complete LOVD gene record after normalizing the HGNC symbol to uppercase and verifying the returned symbol. Returns HGNC/Entrez IDs, chromosome and coordinates, RefSeq transcripts/build, curation details, and dates. Malformed or non-JSON responses are explicit errors.

Parameters:

  • gene_symbol (string) (required) HGNC gene symbol (e.g., ‘TP53’, ‘BRCA1’, ‘BRCA2’, ‘EGFR’).

Example Usage:

query = {
    "name": "LOVD_get_gene",
    "arguments": {
        "gene_symbol": "example_value"
    }
}
result = tu.run(query)

LOVD_get_variants (Type: LOVDTool)#

Get the full unpaginated LOVD variant response for a gene. Every record’s gene symbol and Variant…

LOVD_get_variants tool specification

Tool Information:

  • Name: LOVD_get_variants

  • Type: LOVDTool

  • Description: Get the full unpaginated LOVD variant response for a gene. Every record’s gene symbol and Variant/DNA structure are validated; metadata reports the returned count, completeness basis, and symbol verification. Live TP53 currently returns 880 curated records, including repeated DBIDs when LOVD exposes distinct reports.

Parameters:

  • gene_symbol (string) (required) HGNC gene symbol (e.g., ‘TP53’, ‘BRCA1’).

Example Usage:

query = {
    "name": "LOVD_get_variants",
    "arguments": {
        "gene_symbol": "example_value"
    }
}
result = tu.run(query)

LOVD_search_variants (Type: LOVDTool)#

Search LOVD variants by exactly one DBID or HGVS DNA notation. The wrapper verifies every returne…

LOVD_search_variants tool specification

Tool Information:

  • Name: LOVD_search_variants

  • Type: LOVDTool

  • Description: Search LOVD variants by exactly one DBID or HGVS DNA notation. The wrapper verifies every returned DBID/DNA value and gene symbol. LOVD’s HTTP 404 plus empty array for a valid no-match filter is normalized to a successful empty result, distinct from a malformed response. RefSeq-prefixed returned DNA values are matched to the requested suffix.

Parameters:

  • gene_symbol (string) (required) HGNC gene symbol (e.g., ‘TP53’, ‘BRCA1’).

  • variant_dbid (string) (optional) LOVD variant DBID (e.g., ‘TP53_010464’). Unique identifier assigned by LOVD.

  • dna_notation (string) (optional) HGVS DNA notation without RefSeq prefix (e.g., ‘c.*2609C>A’, ‘c.742C>T’). Use coding ‘c.’ notation.

Example Usage:

query = {
    "name": "LOVD_search_variants",
    "arguments": {
        "gene_symbol": "example_value"
    }
}
result = tu.run(query)