Folklore Clinical Variant Interpretation MCP

Bioinformatics MCP for genomic variant interpretation, gene-disease evidence and literature.

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What it can do

    What data it sees

    Do you need an account

    No: the server works without sign-in

    Bioinformatics MCP for genomic variant interpretation, gene-disease evidence and literature.

    How to connect

    How to connect Folklore Clinical Variant Interpretation MCP to Claude

    The server address to paste into Claude settings:

    https://api.helena.bio/folklore/v1/mcp

    1. Open Claude (claude.ai or the desktop app).
    2. Go to Settings → Connectors.
    3. Click Add custom connector.
    4. Paste the server address copied below into Remote MCP server URL and click Add.
    5. In a chat, click + → Connectors and switch the new connector on.

    Custom connectors are available on Free, Pro, Max, Team and Enterprise plans (Free is limited to one). On Team and Enterprise an organization Owner adds the connector first under Organization settings → Connectors.

    Authorization

    After you click Add, a sign-in window for the service opens. Sign in with your own account and approve access. Claude never sees your password.

    How to connect Folklore Clinical Variant Interpretation MCP to ChatGPT

    The server address to paste into ChatGPT settings:

    https://api.helena.bio/folklore/v1/mcp

    1. Open ChatGPT in a browser (chatgpt.com). A Plus, Pro, Business, Enterprise or Edu plan is required.
    2. Turn on developer mode once: Settings → Apps → Advanced settings → Developer mode.
    3. Open Settings → Connectors and click Create.
    4. Fill in the form: Name (anything), Description (one line about what the service does), MCP server URL (copy it below).
    5. Under Authentication choose OAuth if the service requires sign-in, otherwise None. Click Create.
    6. In a new chat open + → Apps/Connectors and enable the connector.

    OpenAI has renamed this section before (Connectors → Apps/Plugins). If the label differs, search settings for "developer mode". On Business/Enterprise workspaces an admin must allow custom connectors first.

    Authorization

    On first use ChatGPT opens the service's sign-in window. Sign in and approve access.

    How to connect Folklore Clinical Variant Interpretation MCP to Cursor

    The server address to paste into Cursor settings:

    https://api.helena.bio/folklore/v1/mcp

    Fastest: click Open in Cursor below and confirm the prompt.

    Manually:

    1. In Cursor open Settings → Cursor Settings → MCP and click Add new global MCP server.
    2. Paste the JSON copied below into ~/.cursor/mcp.json (per project: .cursor/mcp.json in the repo root).
    3. Save the file. The server appears in the MCP list; authorize it there if asked.

    Authorization

    If the service needs sign-in, an authorize button appears next to the server in the MCP list.

    Server tool list (7)

    Raw names from tools/list. Only developers need these.

    search_variant_evidenceInterpret 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.
    search_variant_literatureResolve 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.
    get_publication_detailsRetrieve 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.
    search_literature_corpusSemantically 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.
    support_helenaLearn 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.
    get_gene_disease_associationsFind 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.
    search_disease_genesFind 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.