Litvar Tools

Configuration File: litvar_tools.json Tool Type: Local Tools Count: 2

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

Available Tools

LitVar_get_variant_publications (Type: BaseRESTTool)

Get PubMed publication IDs (PMIDs) that mention a specific genetic variant, from NCBI LitVar2. Re…

LitVar_get_variant_publications tool specification

Tool Information:

  • Name: LitVar_get_variant_publications

  • Type: BaseRESTTool

  • Description: Get PubMed publication IDs (PMIDs) that mention a specific genetic variant, from NCBI LitVar2. Requires the variant rsID. Returns a list of PubMed IDs and PMC IDs where the variant is mentioned. The max parameter controls the maximum number of PMIDs returned. Use LitVar_search_variants first to find variant rsIDs.

Parameters:

  • rsid (string) (required) dbSNP rsID of the variant (e.g., ‘rs328’, ‘rs7903146’, ‘rs429358’, ‘rs80357906’)

  • format (string) (optional) Response format (default ‘json’)

  • max (integer) (optional) Maximum number of PMIDs to return (default 50)

Example Usage:

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

LitVar_search_variants (Type: BaseRESTTool)

Search for genetic variants in the NCBI LitVar2 database by rsID, gene name, or HGVS notation. Li…

LitVar_search_variants tool specification

Tool Information:

  • Name: LitVar_search_variants

  • Type: BaseRESTTool

  • Description: Search for genetic variants in the NCBI LitVar2 database by rsID, gene name, or HGVS notation. LitVar2 links genetic variants to their mentions in PubMed literature. Returns variant identifiers, associated gene names, HGVS nomenclature, publication counts, and clinical significance when available. Useful for finding which variants have been studied for a gene or identifying literature-linked variants by rsID.

Parameters:

  • query (string) (required) Search query: rsID (e.g., ‘rs328’, ‘rs7903146’), gene name (e.g., ‘BRCA1’, ‘TP53’), or HGVS notation (e.g., ‘p.V600E’)

Example Usage:

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