LitVar2¶
LitVar2 is NCBI's variant-to-literature index: it resolves a variant (a gene plus protein change, or an rsID) to the papers that name it. In BioMCP, LitVar2 is one of the variant article sources: variant articles asks it beside PubTator3's annotation route and merges the linked PMIDs into the union result with litvar source attribution, so variant papers the text and annotation routes miss still appear.
The match is exact. BioMCP keeps only a LitVar2 autocomplete entry whose gene and protein change, or rsID, matches the request through the same variant identity comparison the other routes use, so a reply naming BRAF p.V600K for a p.V600E request contributes nothing. A LitVar2 failure degrades that source only; the search keeps its other routes.
What BioMCP exposes¶
| Command | What BioMCP gets from this source | Integration note |
|---|---|---|
biomcp variant articles "<gene> <protein change>" |
The PMIDs LitVar2 links to the matched variant, merged into the union rows | Runs in the default union and the --strategy annotation strategy |
biomcp variant articles <rsID> |
The PMIDs LitVar2 links to the rsID, merged into the union rows | Works when the rsID itself carries no other alias |
--disable-sources litvar2 |
Nothing; the source never answers | The route reports unavailable naming the setting |
Example commands¶
Merges the 39 papers LitVar2 links to rs372266620 (CDKN2A p.A57V) beside the text and annotation routes, each merged row carrying the litvar source and litvar_variant route.
Resolves the rsID through LitVar2's autocomplete and merges the linked BRAF p.V600E literature with PubTator's annotated papers.
Returns the LitVar2-linked papers for a bare rsID whose MyVariant resolution is indeterminate, where the annotation route alone cannot run.
API access¶
No BioMCP API key required. BioMCP uses NCBI's public LitVar2 API
(variant/autocomplete and variant/get/<variant id>/publications) without a
key.
Official source¶
LitVar2 is NCBI's public variant-literature search. BioMCP uses the public LitVar2 API for the surfaces described here.