Folklore Clinical Variant Interpretation MCP

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io.github.helena-bioinformatics/folklorev1.5.0

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

Health & Science

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

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get_gene_disease_associations Read-only

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.

genestring, required

One public human gene symbol or HGNC identifier, for example BRCA1 or HGNC:1100. No patient data.

limitinteger

Maximum number of source assertions per page, from 1 to 50.

offsetinteger

Zero-based assertion offset; use the returned nextOffset when present.

Tools (7)

get_gene_disease_associations

read-only

Argument	Type	Description
gene*	string	One public human gene symbol or HGNC identifier, for example BRCA1 or HGNC:1100. No patient data.
limit	integer	Maximum number of source assertions per page, from 1 to 50.
offset	integer	Zero-based assertion offset; use the returned nextOffset when present.

Input schema (JSON)

{
  "type": "object",
  "title": "GetGeneDiseaseArguments",
  "required": [
    "gene"
  ],
  "properties": {
    "gene": {
      "type": "string",
      "title": "Gene",
      "maxLength": 64,
      "minLength": 1,
      "description": "One public human gene symbol or HGNC identifier, for example BRCA1 or HGNC:1100. No patient data."
    },
    "limit": {
      "type": "integer",
      "title": "Limit",
      "default": 20,
      "maximum": 50,
      "minimum": 1,
      "description": "Maximum number of source assertions per page, from 1 to 50."
    },
    "offset": {
      "type": "integer",
      "title": "Offset",
      "default": 0,
      "maximum": 1000,
      "minimum": 0,
      "description": "Zero-based assertion offset; use the returned nextOffset when present."
    }
  },
  "additionalProperties": false
}

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.

read-only

Argument	Type	Description
pmid*	string	One PubMed identifier to look up in Folklore's current corpus, as 1 to 12 digits without a PMID prefix.

Input schema (JSON)

{
  "type": "object",
  "title": "GetPublicationDetailsArguments",
  "required": [
    "pmid"
  ],
  "properties": {
    "pmid": {
      "type": "string",
      "title": "Pmid",
      "pattern": "^[0-9]{1,12}$",
      "description": "One PubMed identifier to look up in Folklore's current corpus, as 1 to 12 digits without a PMID prefix."
    }
  },
  "additionalProperties": false
}

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.

read-only

Argument	Type	Description
limit	integer	Maximum number of source assertions per page, from 1 to 50.
offset	integer	Zero-based assertion offset; use the returned nextOffset when present.
disease*	string	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.

Input schema (JSON)

{
  "type": "object",
  "title": "SearchDiseaseGenesArguments",
  "required": [
    "disease"
  ],
  "properties": {
    "limit": {
      "type": "integer",
      "title": "Limit",
      "default": 20,
      "maximum": 50,
      "minimum": 1,
      "description": "Maximum number of source assertions per page, from 1 to 50."
    },
    "offset": {
      "type": "integer",
      "title": "Offset",
      "default": 0,
      "maximum": 1000,
      "minimum": 0,
      "description": "Zero-based assertion offset; use the returned nextOffset when present."
    },
    "disease": {
      "type": "string",
      "title": "Disease",
      "maxLength": 160,
      "minLength": 3,
      "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."
    }
  },
  "additionalProperties": false
}

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.

read-only

Argument	Type	Description
sort	string	Result ordering: relevance-ranked, newest publication first, or oldest publication first.
limit	integer	Maximum number of publications to return, from 1 to 25.
query*	string	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.
cursor	any	Opaque continuation cursor from the preceding response for the same query and sort order; omit for the first page.

Input schema (JSON)

{
  "type": "object",
  "title": "SearchCorpusArguments",
  "required": [
    "query"
  ],
  "properties": {
    "sort": {
      "enum": [
        "relevance",
        "newest",
        "oldest"
      ],
      "type": "string",
      "title": "Sort",
      "default": "relevance",
      "description": "Result ordering: relevance-ranked, newest publication first, or oldest publication first."
    },
    "limit": {
      "type": "integer",
      "title": "Limit",
      "default": 20,
      "maximum": 25,
      "minimum": 1,
      "description": "Maximum number of publications to return, from 1 to 25."
    },
    "query": {
      "type": "string",
      "title": "Query",
      "maxLength": 200,
      "minLength": 3,
      "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."
    },
    "cursor": {
      "anyOf": [
        {
          "type": "string",
          "pattern": "^[A-Za-z0-9_-]+$",
          "maxLength": 128,
          "minLength": 8
        },
        {
          "type": "null"
        }
      ],
      "title": "Cursor",
      "default": null,
      "description": "Opaque continuation cursor from the preceding response for the same query and sort order; omit for the first page."
    }
  },
  "additionalProperties": false
}

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. Never invent or swap REF/ALT, guess a transcript accession, or relabel another assembly as GRCh38. For reference_mismatch, ask the user to verify the source assembly, position, reference and accession version; preserve the refusal. A bare protein consequence needs a gene or versioned protein accession. A report row may include matching genomic, coding and protein descriptions with a versioned transcript; submit the complete row without discarding conflicting parts. For not_found, preserve the missing exact mapping rather than back-translating a protein change.

read-only

Argument	Type	Description
query*	string	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.
assembly	string	Reference genome assembly. Folklore currently accepts GRCh38 only.

Input schema (JSON)

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.

read-only

Argument	Type	Description
limit	integer	Maximum number of publications to return, from 1 to 25.
query*	string	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.
assembly	string	Reference genome assembly. Folklore currently accepts GRCh38 only.
question	any	Optional natural-language focus applied after the variant is resolved, such as a condition or evidence question; do not put the variant identifier here.

Input schema (JSON)

{
  "type": "object",
  "title": "SearchVariantLiteratureArguments",
  "required": [
    "query"
  ],
  "properties": {
    "limit": {
      "type": "integer",
      "title": "Limit",
      "default": 10,
      "maximum": 25,
      "minimum": 1,
      "description": "Maximum number of publications to return, from 1 to 25."
    },
    "query": {
      "type": "string",
      "title": "Query",
      "maxLength": 512,
      "minLength": 1,
      "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."
    },
    "assembly": {
      "type": "string",
      "const": "GRCh38",
      "title": "Assembly",
      "default": "GRCh38",
      "description": "Reference genome assembly. Folklore currently accepts GRCh38 only."
    },
    "question": {
      "anyOf": [
        {
          "type": "string",
          "maxLength": 500,
          "minLength": 3
        },
        {
          "type": "null"
        }
      ],
      "title": "Question",
      "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."
    }
  },
  "additionalProperties": false
}

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.

read-only

No arguments.

Input schema (JSON)

{
  "type": "object",
  "properties": {},
  "additionalProperties": false
}