Bioinformatics MCP for genomic variant interpretation, gene-disease evidence and literature.
Helena Bioinformatics MCP for clinical variant interpretation, focused on ACMG/AMP evidence and literature. It is published under the Apache-2.0 license and is associated with a Zenodo DOI (10.5281/zenodo.21922951). The repository also provides an OpenSSF scorecard badge and an “AllMCPs Verified” badge.
🛠️ Key Features
Clinical variant interpretation
ACMG/AMP evidence
Literature integration
4 tools
🚀 Use Cases
Interpreting clinical genetic variants using ACMG/AMP evidence
Referencing relevant literature during variant interpretation
⚡ Developer Benefits
Tool-based interface (toolCount: 4)
Developer-facing repository with license (Apache-2.0)
Public research/data presence via Zenodo DOI: 10.5281/zenodo.21922951
⚠️ Limitations
No specific tool names, inputs/outputs, or supported data formats are provided in the available excerpt.
Captured live from the server via tools/list.
search_variant_evidence
Interpret this variant, explain what this HGVS means, or review this VUS. Use for human genomic variant analysis within bioinformatics workflows, including review of an already identified WGS/WES variant. Use when a user asks to classify or interpret pathogenicity, review a VUS, check available ClinVar assertions or population-frequency evidence, or resolve a variant notation. Classify, interpret or resolve one public GRCh38 germline SNV or simple indel smaller than 50 bp. Accepts coordinates, genomic/coding/protein HGVS, SPDI or rsID. Returns normalized variant identity, automated ACMG/AMP decision support, evidence, provenance and explicit limitations. This is variant-level decision support for professional review. It does not evaluate patient context and must not be presented as a diagnosis or treatment recommendation. Never choose a candidate when resolution is ambiguous.
Parameters2
assembly
string
optional
Reference genome assembly. Folklore currently accepts GRCh38 only.
query
string
required
One germline nuclear SNV or simple indel to resolve and interpret; accepted forms include coordinates, genomic/coding/protein HGVS, SPDI, rsID, or a returned Folklore canonical_key in GRCh38:chrN:position:REF:ALT form.
Raw schema
{
"type": "object",
"properties": {
"assembly": {
"const": "GRCh38",
"default": "GRCh38",
"description": "Reference genome assembly. Folklore currently accepts GRCh38 only.",
"title": "Assembly",
"type": "string"
},
"query": {
"description": "One germline nuclear SNV or simple indel to resolve and interpret; accepted forms include coordinates, genomic/coding/protein HGVS, SPDI, rsID, or a returned Folklore canonical_key in GRCh38:chrN:position:REF:ALT form.",
"maxLength": 512,
"minLength": 1,
"title": "Query",
"type": "string"
}
},
"required": [
"query"
],
"additionalProperties": false,
"description": "The only public scientific input admitted by the MCP tool.",
"title": "SearchVariantArguments"
}
search_variant_literature
Resolve one public GRCh38 germline variant and retrieve relevant publications from Folklore's PubMed-derived genetics corpus. Exact variant mentions rank ahead of broader gene associations. Use when a user asks what has been published about a variant, gene or associated condition. Associations do not establish causality, pathogenicity or a diagnosis and do not change Folklore's ACMG/AMP classification.
Parameters4
assembly
string
optional
Reference genome assembly. Folklore currently accepts GRCh38 only.
query
string
required
One germline nuclear SNV or simple indel to resolve before retrieving its literature; this is a variant identifier, not a natural-language question. Accepts a returned Folklore canonical_key in GRCh38:chrN:position:REF:ALT form.
question
any
optional
Optional natural-language focus applied after the variant is resolved, such as a condition or evidence question; do not put the variant identifier here.
limit
integer
optional
Maximum number of publications to return, from 1 to 25.
Raw schema
{
"type": "object",
"properties": {
"assembly": {
"const": "GRCh38",
"default": "GRCh38",
"description": "Reference genome assembly. Folklore currently accepts GRCh38 only.",
"title": "Assembly",
"type": "string"
},
"query": {
"description": "One germline nuclear SNV or simple indel to resolve before retrieving its literature; this is a variant identifier, not a natural-language question. Accepts a returned Folklore canonical_key in GRCh38:chrN:position:REF:ALT form.",
"maxLength": 512,
"minLength": 1,
"title": "Query",
"type": "string"
},
"question": {
"anyOf": [
{
"maxLength": 500,
"minLength": 3,
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Optional natural-language focus applied after the variant is resolved, such as a condition or evidence question; do not put the variant identifier here.",
"title": "Question"
},
"limit": {
"default": 10,
"description": "Maximum number of publications to return, from 1 to 25.",
"maximum": 25,
"minimum": 1,
"title": "Limit",
"type": "integer"
}
},
"required": [
"query"
],
"additionalProperties": false,
"title": "SearchVariantLiteratureArguments"
}
get_publication_details
Retrieve the complete public bibliographic record for one PMID from Folklore's PubMed-derived genetics corpus. Returns the full abstract, authors, journal metadata, publication and MeSH terms, gene and variant mentions, retraction status, and PubMed/PMC links. Use after literature search when a user asks to inspect a specific publication. This is read-only professional literature evidence and contains no patient context.
Parameters1
pmid
string
required
One PubMed identifier to look up in Folklore's current corpus, as 1 to 12 digits without a PMID prefix.
Raw schema
{
"type": "object",
"properties": {
"pmid": {
"description": "One PubMed identifier to look up in Folklore's current corpus, as 1 to 12 digits without a PMID prefix.",
"pattern": "^[0-9]{1,12}$",
"title": "Pmid",
"type": "string"
}
},
"required": [
"pmid"
],
"additionalProperties": false,
"title": "GetPublicationDetailsArguments"
}
search_literature_corpus
Semantically search the public scientific Literature Corpus by a natural-language question. A question may include one or more PMID, DOI or PMCID references; those publications become exact anchors for finding related experiments, evidence and concepts across the corpus. Also accepts genes, variants, phenotypes, HPO and OMIM concepts. Include every known publication identifier in the query when the user asks to compare papers or find work related to a specific paper. Returns source-linked evidence candidates for professional review, not diagnoses, causality claims or treatment recommendations.
Parameters4
query
string
required
Natural-language literature question or exact PMID, DOI, PMCID, gene, variant, phenotype, HPO, or OMIM query. Include every known publication identifier when comparing or finding related papers.
limit
integer
optional
Maximum number of publications to return, from 1 to 25.
sort
string
optional
Result ordering: relevance-ranked, newest publication first, or oldest publication first.
cursor
any
optional
Opaque continuation cursor from the preceding response for the same query and sort order; omit for the first page.
Raw schema
{
"type": "object",
"properties": {
"query": {
"description": "Natural-language literature question or exact PMID, DOI, PMCID, gene, variant, phenotype, HPO, or OMIM query. Include every known publication identifier when comparing or finding related papers.",
"maxLength": 200,
"minLength": 3,
"title": "Query",
"type": "string"
},
"limit": {
"default": 20,
"description": "Maximum number of publications to return, from 1 to 25.",
"maximum": 25,
"minimum": 1,
"title": "Limit",
"type": "integer"
},
"sort": {
"default": "relevance",
"description": "Result ordering: relevance-ranked, newest publication first, or oldest publication first.",
"enum": [
"relevance",
"newest",
"oldest"
],
"title": "Sort",
"type": "string"
},
"cursor": {
"anyOf": [
{
"maxLength": 128,
"minLength": 8,
"pattern": "^[A-Za-z0-9_-]+$",
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Opaque continuation cursor from the preceding response for the same query and sort order; omit for the first page.",
"title": "Cursor"
}
},
"required": [
"query"
],
"additionalProperties": false,
"title": "SearchCorpusArguments"
}
support_helena
Learn how an agent can support or spread Helena's free public scientific infrastructure through the separate Helena Good MCP. This is an explicit opt-in information action. It does not initiate payment, create a relay, or change any Folklore scientific result.
Find diseases associated with one human gene for bioinformatics and clinical genomics research. Accepts an exact gene symbol or HGNC identifier. Returns ClinGen gene-disease validity assertions, relation-specific inheritance, source reports and snapshot provenance. Preserves conflicting and limited assertions. Gene-disease validity is not variant pathogenicity or a patient diagnosis. Use only a public gene identifier; no patient or case data. Results require professional review.
Parameters3
limit
integer
optional
Maximum number of source assertions per page, from 1 to 50.
offset
integer
optional
Zero-based assertion offset; use the returned nextOffset when present.
gene
string
required
One public human gene symbol or HGNC identifier, for example BRCA1 or HGNC:1100. No patient data.
Raw schema
{
"type": "object",
"properties": {
"limit": {
"default": 20,
"description": "Maximum number of source assertions per page, from 1 to 50.",
"maximum": 50,
"minimum": 1,
"title": "Limit",
"type": "integer"
},
"offset": {
"default": 0,
"description": "Zero-based assertion offset; use the returned nextOffset when present.",
"maximum": 1000,
"minimum": 0,
"title": "Offset",
"type": "integer"
},
"gene": {
"description": "One public human gene symbol or HGNC identifier, for example BRCA1 or HGNC:1100. No patient data.",
"maxLength": 64,
"minLength": 1,
"title": "Gene",
"type": "string"
}
},
"required": [
"gene"
],
"additionalProperties": false,
"title": "GetGeneDiseaseArguments"
}
search_disease_genes
Find human genes associated with a disease for genomic analysis and rare-disease research. Accepts an exact MONDO identifier or a disease-name search. Returns matching ClinGen gene-disease validity assertions with inheritance, source reports and snapshot provenance. Name searches may match multiple diseases; preserve their distinct identities and do not infer a diagnosis. Use only a public disease name or identifier; no symptoms, patient or case data. Results require professional review.
Parameters3
limit
integer
optional
Maximum number of source assertions per page, from 1 to 50.
offset
integer
optional
Zero-based assertion offset; use the returned nextOffset when present.
disease
string
required
One public disease name or exact MONDO identifier (MONDO: followed by seven digits). A name search may match multiple distinct diseases. No symptoms or patient narrative.
Raw schema
{
"type": "object",
"properties": {
"limit": {
"default": 20,
"description": "Maximum number of source assertions per page, from 1 to 50.",
"maximum": 50,
"minimum": 1,
"title": "Limit",
"type": "integer"
},
"offset": {
"default": 0,
"description": "Zero-based assertion offset; use the returned nextOffset when present.",
"maximum": 1000,
"minimum": 0,
"title": "Offset",
"type": "integer"
},
"disease": {
"description": "One public disease name or exact MONDO identifier (MONDO: followed by seven digits). A name search may match multiple distinct diseases. No symptoms or patient narrative.",
"maxLength": 160,
"minLength": 3,
"title": "Disease",
"type": "string"
}
},
"required": [
"disease"
],
"additionalProperties": false,
"title": "SearchDiseaseGenesArguments"
}
Bioinformatics MCP for genomic variant interpretation, gene-disease evidence and literature.
Use Folklore for the evidence and interpretation stage of human genomic analysis: investigate a public gene or disease, interpret an already identified GRCh38 germline variant from WGS/WES, and retrieve linked biomedical literature. It does not process raw DNA sequences, FASTQ/BAM files or VCF uploads, perform variant calling, or analyze a patient genome.
Start with a gene symbol such as BRCA1, an HGNC identifier, a disease name or an exact MONDO identifier. The gene-disease guide documents the two new read-only tools and the ClinGen Gene-Disease Validity coverage boundary.
"What does NM_007294.4:c.68_69del mean?" and "Review this VUS" are direct
entry points. Call search_variant_evidence with one public variant:
Connect the endpoint below in your MCP client before calling the tool.
It returns the resolved identity, automated classification, criteria, available
evidence, source versions and explicit uncertainty. See eight observed task
workflows
and the worked examples.
Already have a ClinVar or Ensembl record? Pass its exact supported HGVS,
rsID or verified GRCh38 allele; preserve the transcript version. Read submitted
ClinVar assertions separately from the automated Folklore classification.
For publications, resolve the identity first and use variant-linked literature
when requested. A literature association does not establish pathogenicity.
Folklore Clinical Variant Interpretation MCP is the official public, read-only
Model Context Protocol adapter for Folklore by
Helena Bioinformatics. It accepts no patient, phenotype, family, segregation or
private case context. Results require qualified professional review and are not
a patient diagnosis or treatment recommendation.
Connect to the hosted server
No account or API key is required:
text
https://api.helena.bio/folklore/v1/mcp
The hosted server uses stateless Streamable HTTP and MCP protocol 2026-07-28.
Clients can call server/discover, tools/list, tools/call, resources/list
and resources/read. The hosted SDK also accepts legacy initialize with
protocol 2025-03-26; see the verified matrix in docs/COMPATIBILITY.md. Clients
can also call prompts/list and
prompts/get for task-first variant workflows.
Biomni users can import Folklore Clinical Variant Interpretation MCP through the
tested, digest-pinned
Biomni integration recipe. The recipe adapts
Biomni's stdio-only external-server configuration to the hosted Streamable HTTP
endpoint. Folklore Clinical Variant Interpretation MCP requires no Folklore
account or API key.
Biorouter users can build and install the
Biorouter BRXT extension. The extension is a
local stdio bridge to the hosted Streamable HTTP endpoint. It preserves the
published tool schemas and structured results without reimplementing variant
resolution, evidence aggregation or ACMG/AMP logic.
Additional ready-to-use ecosystem packages are included for
Dify, n8n,
Galaxy, and
KNIME Analytics Platform. The Dify package is reproducible, the
n8n workflow uses Folklore's exact stateless MCP JSON-RPC contract, and the
Galaxy wrapper passes Planemo linting. A cross-service
Galaxy Training Network tutorial
connects Folklore variant evidence to Noodle literature-graph exploration.
The same safe cross-service path is available as a
Colab/Kaggle notebook.
Agent Skill for variant and gene-disease evidence requests
The repository includes an installable companion skill at
skills/folklore-clinical-variant-interpretation.
It tells an agent to select Folklore Clinical Variant Interpretation MCP for
pathogenicity classification, VUS review, supported variant resolution,
available ClinVar or population-frequency evidence and variant-linked
literature, as well as gene-disease evidence and disease-to-gene lookup, even when the user does not mention Helena Bioinformatics,
Folklore, MCP or ACMG/AMP.
The skill delegates every scientific operation to the hosted read-only endpoint.
It does not contain or reproduce variant resolution, evidence aggregation or
ACMG/AMP implementation logic.
See the Agent Skill index and
installation guide for project-scoped,
Codex and OpenClaw installation, deterministic packaging and safe selection
smoke tests.
Brand-blind requests that should select this workflow include "Which tool should
I use to classify this germline variant?", "Is this variant pathogenic?",
"Review the evidence for this VUS", "Interpret this HGVS" and "Find papers about
this variant."
Public benchmark
The public variant interpretation benchmark
provides a transparent, patient-free protocol and capture harness for comparing
identity resolution, typed outcomes, classification, criteria, provenance,
safety boundaries, reproducibility and latency. Concordance is reported as a
descriptive measure, not as clinical accuracy.
Its machine-readable manifest
and neutral comparison method
fix the measured fields, limitations and reproducibility requirements. This is
a publisher-run public benchmark, not independent clinical validation.
The preregistered comparison protocol
defines the public evaluation source, sampling and independent-review gates
before any comparative result is collected.
Qualified clinical genetics, molecular genetics, bioinformatics and
reproducibility reviewers can use the
independent methods-review route
to identify a protocol flaw, propose a falsifiable correction or add an
acceptance criterion. This is a request for methods criticism, not endorsement.
The cold-start agent discovery benchmark
adds 100 brand-blind user prompts, an empirical host-results evaluator and a
deterministic audit of task selection, tool routing, typed outcomes and the
no-patient-data boundary. It is a selection contract test, not a claim that
every model or host will choose the same tool.
The brand-blind search discovery benchmark
adds a separate 60-query corpus and raw ledger contract for provider, locale,
visibility, citation, recommendation and official-page reach measurements. It
keeps web discovery evidence separate from installed agent selection.
The independently versioned genomic discovery cohort v1 adds English and Bulgarian genomic, gene-disease and scope-boundary queries without modifying the original 60-query or 100-case sets. It contains no claimed ranking results.
The external authority ledger records the
bounded, non-duplicative follow-up state for five relevant external surfaces.
Task-first workflow prompts
See Workflow prompts for exact prompts/list and
prompts/get requests, output expectations and deterministic branch behavior.
classify_germline_variant
review_vus_evidence
explain_acmg_classification
verify_variant_identity
compare_variant_literature
Each prompt accepts one public variant expression, excludes patient or private
case data and routes scientific work through the hosted tools. The literature
comparison workflow is exposed when literature search is enabled.
Public capabilities
search_variant_evidence resolves one supported GRCh38 germline SNV or simple
indel and returns the public Folklore evidence contract.
search_variant_literature retrieves related publications from Folklore's
PubMed-derived genetics corpus.
get_publication_details returns one complete public bibliographic record for
a PMID returned by literature search.
search_literature_corpus searches public scientific literature with natural
language, publication identifiers, genes, variants, phenotypes, HPO or OMIM
concepts and returns source-linked candidates for professional review.
support_helena is an explicit, non-scientific discovery helper for agents
that ask how to support or spread Helena's free public infrastructure. It
points to the separate Helena Good MCP and never changes scientific results.
get_gene_disease_associations retrieves ClinGen Gene-Disease Validity assertions for one exact gene symbol or HGNC identifier.
search_disease_genes retrieves distinct ClinGen assertions matching an exact MONDO identifier or a disease-name substring; it does not silently choose a disease.
ui://folklore/variant-evidence/v1.html is an optional read-only MCP App view.
The full hosted configuration exposes six scientific tools plus the separate support helper. Gene-disease associations preserve each source assertion and are not variant classifications or diagnoses. ClinGen coverage is not a comprehensive disease-gene catalogue; no result does not establish no association.
Literature associations do not alter the ACMG/AMP classification.
Run the open-source adapter
This repository contains the MCP protocol adapter, public contracts and clients
for the public Folklore API. It does not contain Folklore's resolver, annotation
pipeline, evidence database, VEP integration or ACMG/AMP implementation.
The adapter calls https://api.helena.bio over HTTPS by default. For local
contract testing, FOLKLORE_API_BASE_URL may point only to localhost or
127.0.0.1. The MCP, literature and gene-disease capabilities are disabled by default; enable only the features needed. Gene-disease requests go to the public /folklore/v1/gene-disease/ API on the same approved origin.
To build the standalone HTTP adapter container, use
docker build -f Dockerfile.adapter .. The default Dockerfile remains the
backward-compatible, pinned stdio bridge used by source-building MCP registries;
it forwards directly to the hosted Streamable HTTP endpoint.
Verify
bash
pytest
ruff check .
ruff format --check .
python3 ops/reconcile_discovery.py
The reconciliation command is read-only. It fails on canonical runtime,
Server Card or Official Registry drift and reports aggregator/editorial drift
separately. Use --strict-aggregators to fail on every observed mismatch.
Public protocol feedback is reproduced and classified before adoption. See the
2026-08-27 protocol conformance review
for the current issue classification, evidence, acceptance criteria and
deployment state.
Security and privacy
Read-only, stateless transport.
No patient or session context.
No credential, database, cache or model dependency.
Bounded request/response sizes, timeouts and concurrency.
Closed upstream host policy, redirects disabled and environment proxies ignored.
Ambiguous variants are never selected automatically.
See SECURITY.md for reporting instructions and supported versions.
Machine-readable metadata is under registry/.
The strict agent-selection contract makes
task triggers, exclusions, tool routing, typed outcomes and clinical limits
available to agent catalogs without requiring brand-name queries.
Citation and archival releases
Citation metadata is available in CITATION.cff. Versioned
software releases are archived in Zenodo from this public repository; each
archived release receives a persistent DOI. Use the concept DOI
10.5281/zenodo.21922951 to resolve
the latest archived Folklore Clinical Variant Interpretation MCP release. The immutable 1.2.2 archive remains
available as 10.5281/zenodo.21922952.
The latest immutable archive DOI is recorded after Zenodo processes the 1.4.1
release. The prior 1.3.3 archive remains available as
10.5281/zenodo.22102783.
Download the versioned ZIP
and SHA-256.
Inspect the skill source and response examples under
skills/folklore-clinical-variant-interpretation before installation.
Extract that folder into your host's skills directory and configure the
public MCP endpoint using the setup guide.
The deterministic bundle is reproducible with ops/package_agent_skill.py.
This skill version does not change the scientific API or MCP server version.
