Litvar Tools#

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

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

Available Tools#

LitVar_get_variant_details (Type: BaseRESTTool)#

Get the full structured variant record from NCBI LitVar2 by rsID (the ‘variant/get’ endpoint, WIT…

LitVar_get_variant_details tool specification

Tool Information:

  • Name: LitVar_get_variant_details

  • Type: BaseRESTTool

  • Description: Get the full structured variant record from NCBI LitVar2 by rsID (the ‘variant/get’ endpoint, WITHOUT the publications list). Given a dbSNP rsID, returns a single normalized record combining: ClinGen canonical allele IDs (CA…), associated gene(s), variant name and HGVS notation, genomic chromosome:position (data_chromosome_base_position), allele, SNP class (e.g. snv), species and NCBI tax id, the literature-derived clinical-significance set (data_clinical_significance), and, when available, ALFA minor allele frequency (data_maf). This is the variant ‘profile’ record - use LitVar_get_variant_publications for the list of citing PMIDs, or LitVar_search_variants to find an rsID from a gene or HGVS query.

Parameters:

  • rsid (string) (required) dbSNP rsID of the variant (e.g., ‘rs113488022’ = BRAF V600E, ‘rs121913529’ = KRAS G12, ‘rs328’, ‘rs7903146’). Provide the rsID only; the litvar@…## wrapper is added automatically.

Example Usage:

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

LitVar_get_variant_publications (Type: BaseRESTTool)#

Get PubMed and PubMed Central publication IDs that mention a variant in NCBI LitVar2. LitVar2 ign…

LitVar_get_variant_publications tool specification

Tool Information:

  • Name: LitVar_get_variant_publications

  • Type: BaseRESTTool

  • Description: Get PubMed and PubMed Central publication IDs that mention a variant in NCBI LitVar2. LitVar2 ignores max/limit/offset and returns complete ID lists, so this wrapper applies offset/max locally and reports exact PMID and PMCID totals plus next_offset. Use LitVar_search_variants first to find an rsID.

Parameters:

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

  • format (string) (optional) Compatibility option; LitVar2 returns JSON and only ‘json’ is accepted.

  • max (integer) (optional) Maximum IDs returned from each of the PMID and PMCID lists on this local page (default 50, max 1000).

  • offset (integer) (optional) Zero-based local offset into both complete ID lists. Use metadata.next_offset to continue.

Example Usage:

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

LitVar_search_variants (Type: BaseRESTTool)#

Retrieve LitVar2 autocomplete top-N variant candidates by rsID, gene, or HGVS text. This is not a…

LitVar_search_variants tool specification

Tool Information:

  • Name: LitVar_search_variants

  • Type: BaseRESTTool

  • Description: Retrieve LitVar2 autocomplete top-N variant candidates by rsID, gene, or HGVS text. This is not an exhaustive paginated search: the endpoint honors limit up to 100 but ignores offset. If metadata.upstream_truncated is true, additional candidates may exist and the query must be narrowed or limit increased.

Parameters:

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

  • limit (integer) (optional) Maximum autocomplete candidates (default 10, max 100). The endpoint does not support offset pagination.

Example Usage:

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