Searches public scientific literature and retrieves variant-related publications and bibliographic records, including by PMID, from Folklore's PubMed-derived corpus.
Version 1.7.0
Folklore MCP classifies and assesses germline variants under ACMG/AMP. It returns canonical identity, automated classification, reported criteria, annotation, source evidence and provenance. Gene profiles, ClinGen gene-disease assertions and linked biomedical literature complete the scientific workflow.
Connect your MCP client to:
https://api.helena.bio/folklore/v1/mcpAccess is anonymous. Call classify_germline_variant:
{"name":"classify_germline_variant","arguments":{"assembly":"GRCh38","query":"NM_007294.4:c.68_69del"}}Input: one public GRCh38 nuclear germline SNV or simple indel smaller than 50 bp. Accepted notation includes supported HGVS, SPDI, rsID and genomic coordinates. Preserve transcript versions and reference alleles.
A resolved identity with successful interpretation includes automated ACMG/AMP classification, reported criteria, annotations, source evidence and provenance. Submitted ClinVar assertions retain their own source attribution alongside the Folklore classification. A VUS is a classification outcome.
Status | Next step |
| Read interpretation status, then classification and evidence. |
| Present candidates for an explicit allele choice. |
| Report the source-scoped miss. |
| Supply a corrected supported expression. |
| Select a workflow for the requested variant type or assembly. |
| Inspect the typed error and retry policy. |
Interpretation status is success or unavailable. Transport, JSON-RPC, MCP
and adapter errors have separate fields. See typed outcomes.
Related MCP server: clingen-link
Tool | Operation |
| Resolve, classify and assess one supported germline variant. |
| Retrieve publications linked to a resolved variant. |
| Retrieve the bibliographic record and abstract for a PMID. |
| Search publications by scientific question or public identifier. |
| Retrieve ClinGen assertions for an exact gene symbol or HGNC identifier. |
| Retrieve ClinGen assertions by MONDO identifier or disease-name substring. |
| Resolve a human gene symbol, alias or stable identifier. |
| Read the selected HGNC gene at its returned snapshot. |
| Continue one profile section using its cursor. |
| Retrieve a separate live publication capture for the selected gene. |
ClinGen results preserve assertion-level disease identity, inheritance, validity assessment, panel, date and source links. Profile sections retain provider, assembly, release, units and pagination. Gene literature has its own capture identity. Follow gene-disease and gene-profile contracts for exact inputs.
support_helena provides links to the separate Helena Good service when the
user asks about supporting Helena. An optional MCP App renders variant results.
The hosted server uses stateless Streamable HTTP and MCP 2026-07-28.
Requests carry matching protocol metadata and routing headers. Supported methods
include server/discover, tools/list, tools/call, prompts/list,
prompts/get, resources/list and resources/read.
The compatibility guide records protocol/client observations. All clients sharing egress use the same rate budget.
Install the portable Agent Skill using the installation guide. It routes pathogenicity, VUS, ClinVar, population-frequency, gene-disease and literature tasks to the hosted tools. The skill source includes OpenAI interface metadata.
Workflow prompts compose tool operations for classification, VUS assessment, ACMG/AMP explanation, identity verification and variant-literature comparison. Each accepts one public variant expression.
The Apache-2.0 adapter implements MCP transport, public API clients and validated response projection. Folklore's scientific authorities produce normalization, annotation, evidence aggregation and classification.
python3.12 -m venv .venv
. .venv/bin/activate
pip install -e '.[dev]'
FOLKLORE_MCP_ENABLED=true \
FOLKLORE_LITERATURE_ENABLED=true \
FOLKLORE_GENE_DISEASE_ENABLED=true \
FOLKLORE_PUBLIC_GENE_ENABLED=true \
folklore-mcpCapabilities are enabled through the flags above. Gene literature requires both
public-gene and literature capabilities. The default upstream is
https://api.helena.bio; local contract tests support localhost and
127.0.0.1. The standalone HTTP image uses Dockerfile.adapter; Dockerfile
provides the pinned stdio bridge.
pytest
ruff check .
ruff format --check .
python3 ops/reconcile_discovery.pyThe read-only reconciler compares runtime, Server Card and Official Registry
state, with separate aggregator observations. python3 ops/public_smoke.py
checks discovery, prompts and resources.
Public measurement sources: variant interpretation, 100-case agent discovery, 60-query search discovery and genomic discovery cohort.
Registry name: io.github.helena-bioinformatics/folklore
Publisher: Helena Bioinformatics
Website: https://folklore.helena.bio
The immutable MCP adapter 1.6.0 archive is
10.5281/zenodo.23817704, from signed tag
folklore-mcp-v1.6.0 at 55a332c6dd6bd4650e921c12ac145b8e0f90476a.
The Biorouter-tag archive is
10.5281/zenodo.23818207.
Apache License 2.0. See LICENSE and NOTICE.
Automated variant classifications support qualified professional review and are not patient diagnoses or treatment recommendations.
This server cannot be deployed
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