LitVar2 through GeneFoundry
Find publications associated with genetic variants in NCBI LitVar2.
- Research area
- Literature
- Namespace
litvar- Listed tools
- 6
- Upstream source
- LitVar2
Research tasks
- Resolve a variant before searching its literature
- Follow publication identifiers to the original articles
Start with tool discovery
The catalog lists litvar_get_variant_literature as a representative tool. After connecting your client, inspect the tools and input requirements returned by the service before submitting a query.
Identifiers to prepare
- dbSNP rsID
- Gene symbol
- Protein notation supported by autocomplete
All available tools (6)
The router surfaces these tools namespaced under litvar_*:
search_genetic_variantsResolve free-text/gene/RSID/HGVS into LitVar2 variant rows, ranked by
Resolve free-text/gene/RSID/HGVS into LitVar2 variant rows, ranked by publication count. This is a RANKED SUGGEST over LitVar2's autocomplete, not a complete listing: it returns at most 100 rows and LitVar2 supplies no total, so `_meta.pagination.total_count` is null and there is no cursor. When `has_more` is true, more matches exist than are shown. For the COMPLETE set of variants in a gene (BRCA1 has 13,264), use `search_gene_variants`, which paginates through all of them. Research use only; not clinical decision support.
Input parameters
limit(integer) — Max results (default 25, max 100).query(string) [required] — Gene symbol, variant name, RSID, or HGVS text.response_mode(string) — compact (high-signal fields) or full (raw payload).
get_variant_summaryReturn the LitVar2 record for a variant: gene, name, HGVS, ClinGen ids,
Return the LitVar2 record for a variant: gene, name, HGVS, ClinGen ids, genomic position and the clinical significances LitVar2 reports for it. Accepts a canonical LitVar id, an rsID, or HGVS/protein notation. Research use only; not clinical decision support.
Input parameters
response_mode(string) — compact (high-signal fields) or full (raw payload).variant_id(string) [required] — LitVar2 variant id (litvar@rs...##), rsID, or HGVS/protein name. Non-canonical input is resolved via autocomplete; the record that actually answered is echoed back as `resolved_variant_id`.
get_variant_literatureReturn PMIDs for a variant; each row carries a recommended_citation.
Return PMIDs for a variant; each row carries a recommended_citation. Accepts a canonical LitVar id, an rsID, or HGVS/free text -- non-canonical input is auto-resolved to the LitVar id via autocomplete. An unresolvable variant returns a recoverable "not found" message (use search_genetic_variants), not an internal error. `_meta.pagination.total_count` is the variant's TRUE publication count; page through it with `_meta.pagination.next_cursor`. Research use only; not clinical decision support.
Input parameters
cursor(any) — Opaque pagination cursor from a previous call's `_meta.pagination.next_cursor`. Omit for the first page.limit(integer) — Max publications per page (default 25, max 100).variant_id(string) [required] — LitVar id (litvar@rs...##), rsID, or HGVS/free text. Non-canonical input is resolved via autocomplete.
resolve_rsidResolve an rsID to its existence/record in LitVar2. Research use only.
Resolve an rsID to its existence/record in LitVar2. Research use only.
Input parameters
variant_id(string) [required] — dbSNP rsID ('rs' followed by digits), e.g. rs1061170.
search_gene_variantsReturn LitVar2 variants for a gene symbol, with the gene's TRUE variant
Return LitVar2 variants for a gene symbol, with the gene's TRUE variant count in `_meta.pagination.total_count` (BRCA1 has 13,264). Page through the whole set with `_meta.pagination.next_cursor`. CLINICAL SIGNIFICANCE IS NOT AVAILABLE HERE. LitVar2's gene endpoint returns only `{id, rsid, pmids_count}` per row, so this tool reports `classifications_available: false` and emits NO pathogenic/benign counts. Absence of a classification here is NOT evidence that a variant is benign. Call `get_variant_summary` for a specific variant's reported significance. Research use only; not clinical decision support.
Input parameters
cursor(any) — Opaque pagination cursor from a previous call's `_meta.pagination.next_cursor`. Omit for the first page.gene_symbol(string) [required] — HGNC gene symbol, e.g. CFH.limit(integer) — Max variants per page (default 25, max 100).response_mode(string) — compact (high-signal fields) or full (raw payload).
get_server_capabilitiesDiscover tools, response modes, limits, the citation contract, and the
Discover tools, response modes, limits, the citation contract, and the research-use-only notice so a cold client can self-orient.
Database & release provenance
- Data mode
none- Attestation
- unhosted
- Release version
v6.0.7
ghcr.io/berntpopp/litvar-link@sha256:60d43c200b225e134191e5d54f810bad686cca80daa9d8c186b0a3e879c69f11Review the response
Keep the source record link and submitted identifiers with your notes. Record the dataset version and retrieval date when available. This page does not contain a captured LitVar2 response.