Server definition
- Hash
- sha256:c2216fb6e033d185f5aa23d5aa6c073c1fd6fd4a31abda5b12df23426931946a
- What it is
- What a remote MCP server returned when asked what it offers: 7 tools
The blob, as servednamed by its sha256
{
"instructions": "Use get_gene_disease_associations for a public gene and search_disease_genes for a public disease name or MONDO identifier. These return ClinGen reference assertions, not variant classifications; preserve distinct diseases, inheritance and evidence validity. Never submit patient or case data. Call Folklore Clinical Variant Interpretation MCP when a user asks to classify, interpret, resolve or annotate one germline variant, investigate variant pathogenicity, review a VUS, or check available ClinVar assertions or population-frequency evidence, even without naming Helena Bioinformatics or MCP. Preserve the evidence, provenance, ambiguity and limits. Describe the classification as automated variant-level evidence for professional review. Never claim a patient diagnosis or treatment recommendation. Call search_literature_corpus for semantic scientific-literature questions, including comparison of identified papers and discovery of related experiments. Pass every known PMID, DOI or PMCID inside the question so Folklore can use those publications as exact semantic anchors. Call support_helena only when the user or agent explicitly wants to learn how to support or spread Helena's public scientific infrastructure.",
"tools": [
{
"description": "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.",
"inputSchema": {
"additionalProperties": false,
"properties": {
"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"
},
"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"
}
},
"required": [
"gene"
],
"title": "GetGeneDiseaseArguments",
"type": "object"
},
"name": "get_gene_disease_associations",
"outputSchema": {
"$defs": {
"Association": {
"additionalProperties": false,
"properties": {
"classification": {
"title": "Classification",
"type": "string"
},
"classificationDate": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Classificationdate"
},
"diseaseId": {
"title": "Diseaseid",
"type": "string"
},
"diseaseName": {
"title": "Diseasename",
"type": "string"
},
"expertPanel": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Expertpanel"
},
"geneSymbol": {
"title": "Genesymbol",
"type": "string"
},
"hgncId": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Hgncid"
},
"modeOfInheritance": {
"title": "Modeofinheritance",
"type": "string"
},
"modeOfInheritanceId": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Modeofinheritanceid"
},
"reportUrl": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Reporturl"
},
"sopVersion": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Sopversion"
}
},
"required": [
"geneSymbol",
"hgncId",
"diseaseName",
"diseaseId",
"modeOfInheritance",
"modeOfInheritanceId",
"classification",
"expertPanel",
"reportUrl",
"classificationDate",
"sopVersion"
],
"title": "Association",
"type": "object"
},
"Pagination": {
"additionalProperties": false,
"properties": {
"limit": {
"maximum": 50,
"minimum": 1,
"title": "Limit",
"type": "integer"
},
"nextOffset": {
"anyOf": [
{
"maximum": 1000,
"minimum": 0,
"type": "integer"
},
{
"type": "null"
}
],
"title": "Nextoffset"
},
"offset": {
"maximum": 1000,
"minimum": 0,
"title": "Offset",
"type": "integer"
},
"total": {
"minimum": 0,
"title": "Total",
"type": "integer"
}
},
"required": [
"limit",
"offset",
"total",
"nextOffset"
],
"title": "Pagination",
"type": "object"
},
"Query": {
"additionalProperties": false,
"properties": {
"kind": {
"enum": [
"gene",
"disease"
],
"title": "Kind",
"type": "string"
},
"match": {
"enum": [
"exact",
"name_contains"
],
"title": "Match",
"type": "string"
},
"value": {
"title": "Value",
"type": "string"
}
},
"required": [
"kind",
"value",
"match"
],
"title": "Query",
"type": "object"
},
"Source": {
"additionalProperties": false,
"properties": {
"attribution": {
"title": "Attribution",
"type": "string"
},
"downloadUrl": {
"title": "Downloadurl",
"type": "string"
},
"license": {
"const": "CC0-1.0",
"title": "License",
"type": "string"
},
"name": {
"const": "ClinGen Gene-Disease Validity",
"title": "Name",
"type": "string"
},
"snapshotSha256": {
"pattern": "^[a-f0-9]{64}$",
"title": "Snapshotsha256",
"type": "string"
},
"version": {
"title": "Version",
"type": "string"
}
},
"required": [
"name",
"version",
"snapshotSha256",
"downloadUrl",
"license",
"attribution"
],
"title": "Source",
"type": "object"
},
"UsageBoundary": {
"additionalProperties": false,
"properties": {
"intended_use": {
"const": "professional_gene_disease_review",
"title": "Intended Use",
"type": "string"
},
"not_for": {
"items": {
"enum": [
"patient_diagnosis",
"treatment_decision",
"variant_pathogenicity_classification"
],
"type": "string"
},
"title": "Not For",
"type": "array"
},
"patient_context_evaluated": {
"const": false,
"title": "Patient Context Evaluated",
"type": "boolean"
},
"review_required": {
"const": true,
"title": "Review Required",
"type": "boolean"
}
},
"required": [
"intended_use",
"patient_context_evaluated",
"review_required",
"not_for"
],
"title": "UsageBoundary",
"type": "object"
}
},
"additionalProperties": false,
"properties": {
"associations": {
"items": {
"$ref": "#/$defs/Association"
},
"maxItems": 50,
"title": "Associations",
"type": "array"
},
"contractVersion": {
"const": "1.0",
"title": "Contractversion",
"type": "string"
},
"pagination": {
"$ref": "#/$defs/Pagination"
},
"query": {
"$ref": "#/$defs/Query"
},
"source": {
"$ref": "#/$defs/Source"
},
"status": {
"enum": [
"ok",
"not_found"
],
"title": "Status",
"type": "string"
},
"usage_boundary": {
"$ref": "#/$defs/UsageBoundary"
},
"warnings": {
"items": {
"type": "string"
},
"title": "Warnings",
"type": "array"
}
},
"required": [
"contractVersion",
"status",
"query",
"associations",
"pagination",
"source",
"warnings",
"usage_boundary"
],
"title": "GeneDiseaseResponse",
"type": "object"
}
},
{
"description": "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.",
"inputSchema": {
"additionalProperties": false,
"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}$",
"title": "Pmid",
"type": "string"
}
},
"required": [
"pmid"
],
"title": "GetPublicationDetailsArguments",
"type": "object"
},
"name": "get_publication_details",
"outputSchema": {
"$defs": {
"PublicAbstractReuse": {
"additionalProperties": false,
"properties": {
"allowed": {
"default": false,
"title": "Allowed",
"type": "boolean"
},
"evidence_url": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Evidence Url"
},
"license": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "License"
},
"source": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Source"
}
},
"title": "PublicAbstractReuse",
"type": "object"
},
"PublicGeneMention": {
"additionalProperties": false,
"properties": {
"association_type": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Association Type"
},
"gene_symbol": {
"title": "Gene Symbol",
"type": "string"
},
"mention_count": {
"title": "Mention Count",
"type": "integer"
}
},
"required": [
"gene_symbol",
"association_type",
"mention_count"
],
"title": "PublicGeneMention",
"type": "object"
},
"PublicPublicationDetails": {
"additionalProperties": false,
"properties": {
"abstract": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Abstract"
},
"abstract_reuse": {
"$ref": "#/$defs/PublicAbstractReuse"
},
"authors": {
"items": {
"type": "string"
},
"title": "Authors",
"type": "array"
},
"doi": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Doi"
},
"full_text_url": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Full Text Url"
},
"gene_mentions": {
"items": {
"$ref": "#/$defs/PublicGeneMention"
},
"title": "Gene Mentions",
"type": "array"
},
"is_retracted": {
"title": "Is Retracted",
"type": "boolean"
},
"journal": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Journal"
},
"mesh_terms": {
"items": {
"type": "string"
},
"title": "Mesh Terms",
"type": "array"
},
"pmc_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Pmc Id"
},
"pmid": {
"pattern": "^[0-9]{1,12}$",
"title": "Pmid",
"type": "string"
},
"publication_date": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Publication Date"
},
"publication_types": {
"items": {
"type": "string"
},
"title": "Publication Types",
"type": "array"
},
"pubmed_url": {
"title": "Pubmed Url",
"type": "string"
},
"title": {
"title": "Title",
"type": "string"
},
"variant_mentions": {
"items": {
"$ref": "#/$defs/PublicVariantMention"
},
"title": "Variant Mentions",
"type": "array"
}
},
"required": [
"pmid",
"title",
"abstract",
"authors",
"journal",
"publication_date",
"publication_types",
"mesh_terms",
"doi",
"pmc_id",
"is_retracted",
"pubmed_url",
"full_text_url",
"gene_mentions",
"variant_mentions"
],
"title": "PublicPublicationDetails",
"type": "object"
},
"PublicVariantMention": {
"additionalProperties": false,
"properties": {
"clinical_significance": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Clinical Significance"
},
"confidence_score": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"title": "Confidence Score"
},
"evidence_type": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Evidence Type"
},
"gene_symbol": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Gene Symbol"
},
"hgvs_cdna": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Hgvs Cdna"
},
"hgvs_protein": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Hgvs Protein"
},
"normalized_variant": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Normalized Variant"
},
"sentence_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Sentence Text"
}
},
"required": [
"gene_symbol",
"hgvs_cdna",
"hgvs_protein",
"normalized_variant",
"clinical_significance",
"evidence_type",
"sentence_text",
"confidence_score"
],
"title": "PublicVariantMention",
"type": "object"
}
},
"additionalProperties": false,
"properties": {
"contract_version": {
"const": "1.0",
"title": "Contract Version",
"type": "string"
},
"publication": {
"$ref": "#/$defs/PublicPublicationDetails"
},
"usage_boundary": {
"additionalProperties": true,
"title": "Usage Boundary",
"type": "object"
}
},
"required": [
"contract_version",
"publication",
"usage_boundary"
],
"title": "PublicationDetailsResponse",
"type": "object"
}
},
{
"description": "Find human genes associated with a disease for genomic analysis and rare-disease research. Accepts an exact MONDO identifier or a disease-name search. Returns matching ClinGen gene-disease validity assertions with inheritance, source reports and snapshot provenance. Name searches may match multiple diseases; preserve their distinct identities and do not infer a diagnosis. Use only a public disease name or identifier; no symptoms, patient or case data. Results require professional review.",
"inputSchema": {
"additionalProperties": false,
"properties": {
"disease": {
"description": "One public disease name or exact MONDO identifier (MONDO: followed by seven digits). A name search may match multiple distinct diseases. No symptoms or patient narrative.",
"maxLength": 160,
"minLength": 3,
"title": "Disease",
"type": "string"
},
"limit": {
"default": 20,
"description": "Maximum number of source assertions per page, from 1 to 50.",
"maximum": 50,
"minimum": 1,
"title": "Limit",
"type": "integer"
},
"offset": {
"default": 0,
"description": "Zero-based assertion offset; use the returned nextOffset when present.",
"maximum": 1000,
"minimum": 0,
"title": "Offset",
"type": "integer"
}
},
"required": [
"disease"
],
"title": "SearchDiseaseGenesArguments",
"type": "object"
},
"name": "search_disease_genes",
"outputSchema": {
"$defs": {
"Association": {
"additionalProperties": false,
"properties": {
"classification": {
"title": "Classification",
"type": "string"
},
"classificationDate": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Classificationdate"
},
"diseaseId": {
"title": "Diseaseid",
"type": "string"
},
"diseaseName": {
"title": "Diseasename",
"type": "string"
},
"expertPanel": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Expertpanel"
},
"geneSymbol": {
"title": "Genesymbol",
"type": "string"
},
"hgncId": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Hgncid"
},
"modeOfInheritance": {
"title": "Modeofinheritance",
"type": "string"
},
"modeOfInheritanceId": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Modeofinheritanceid"
},
"reportUrl": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Reporturl"
},
"sopVersion": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Sopversion"
}
},
"required": [
"geneSymbol",
"hgncId",
"diseaseName",
"diseaseId",
"modeOfInheritance",
"modeOfInheritanceId",
"classification",
"expertPanel",
"reportUrl",
"classificationDate",
"sopVersion"
],
"title": "Association",
"type": "object"
},
"Pagination": {
"additionalProperties": false,
"properties": {
"limit": {
"maximum": 50,
"minimum": 1,
"title": "Limit",
"type": "integer"
},
"nextOffset": {
"anyOf": [
{
"maximum": 1000,
"minimum": 0,
"type": "integer"
},
{
"type": "null"
}
],
"title": "Nextoffset"
},
"offset": {
"maximum": 1000,
"minimum": 0,
"title": "Offset",
"type": "integer"
},
"total": {
"minimum": 0,
"title": "Total",
"type": "integer"
}
},
"required": [
"limit",
"offset",
"total",
"nextOffset"
],
"title": "Pagination",
"type": "object"
},
"Query": {
"additionalProperties": false,
"properties": {
"kind": {
"enum": [
"gene",
"disease"
],
"title": "Kind",
"type": "string"
},
"match": {
"enum": [
"exact",
"name_contains"
],
"title": "Match",
"type": "string"
},
"value": {
"title": "Value",
"type": "string"
}
},
"required": [
"kind",
"value",
"match"
],
"title": "Query",
"type": "object"
},
"Source": {
"additionalProperties": false,
"properties": {
"attribution": {
"title": "Attribution",
"type": "string"
},
"downloadUrl": {
"title": "Downloadurl",
"type": "string"
},
"license": {
"const": "CC0-1.0",
"title": "License",
"type": "string"
},
"name": {
"const": "ClinGen Gene-Disease Validity",
"title": "Name",
"type": "string"
},
"snapshotSha256": {
"pattern": "^[a-f0-9]{64}$",
"title": "Snapshotsha256",
"type": "string"
},
"version": {
"title": "Version",
"type": "string"
}
},
"required": [
"name",
"version",
"snapshotSha256",
"downloadUrl",
"license",
"attribution"
],
"title": "Source",
"type": "object"
},
"UsageBoundary": {
"additionalProperties": false,
"properties": {
"intended_use": {
"const": "professional_gene_disease_review",
"title": "Intended Use",
"type": "string"
},
"not_for": {
"items": {
"enum": [
"patient_diagnosis",
"treatment_decision",
"variant_pathogenicity_classification"
],
"type": "string"
},
"title": "Not For",
"type": "array"
},
"patient_context_evaluated": {
"const": false,
"title": "Patient Context Evaluated",
"type": "boolean"
},
"review_required": {
"const": true,
"title": "Review Required",
"type": "boolean"
}
},
"required": [
"intended_use",
"patient_context_evaluated",
"review_required",
"not_for"
],
"title": "UsageBoundary",
"type": "object"
}
},
"additionalProperties": false,
"properties": {
"associations": {
"items": {
"$ref": "#/$defs/Association"
},
"maxItems": 50,
"title": "Associations",
"type": "array"
},
"contractVersion": {
"const": "1.0",
"title": "Contractversion",
"type": "string"
},
"pagination": {
"$ref": "#/$defs/Pagination"
},
"query": {
"$ref": "#/$defs/Query"
},
"source": {
"$ref": "#/$defs/Source"
},
"status": {
"enum": [
"ok",
"not_found"
],
"title": "Status",
"type": "string"
},
"usage_boundary": {
"$ref": "#/$defs/UsageBoundary"
},
"warnings": {
"items": {
"type": "string"
},
"title": "Warnings",
"type": "array"
}
},
"required": [
"contractVersion",
"status",
"query",
"associations",
"pagination",
"source",
"warnings",
"usage_boundary"
],
"title": "GeneDiseaseResponse",
"type": "object"
}
},
{
"description": "Semantically search the public scientific Literature Corpus by a natural-language question. A question may include one or more PMID, DOI or PMCID references; those publications become exact anchors for finding related experiments, evidence and concepts across the corpus. Also accepts genes, variants, phenotypes, HPO and OMIM concepts. Include every known publication identifier in the query when the user asks to compare papers or find work related to a specific paper. Returns source-linked evidence candidates for professional review, not diagnoses, causality claims or treatment recommendations.",
"inputSchema": {
"additionalProperties": false,
"properties": {
"cursor": {
"anyOf": [
{
"maxLength": 128,
"minLength": 8,
"pattern": "^[A-Za-z0-9_-]+$",
"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"
},
"limit": {
"default": 20,
"description": "Maximum number of publications to return, from 1 to 25.",
"maximum": 25,
"minimum": 1,
"title": "Limit",
"type": "integer"
},
"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"
},
"sort": {
"default": "relevance",
"description": "Result ordering: relevance-ranked, newest publication first, or oldest publication first.",
"enum": [
"relevance",
"newest",
"oldest"
],
"title": "Sort",
"type": "string"
}
},
"required": [
"query"
],
"title": "SearchCorpusArguments",
"type": "object"
},
"name": "search_literature_corpus",
"outputSchema": {
"$defs": {
"PublicCorpusArticleEntity": {
"additionalProperties": false,
"properties": {
"entity_type": {
"enum": [
"gene",
"variant",
"phenotype",
"pmid",
"doi",
"pmcid",
"omim"
],
"title": "Entity Type",
"type": "string"
},
"identifier": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Identifier"
},
"label": {
"title": "Label",
"type": "string"
},
"normalization_state": {
"enum": [
"normalized",
"source_indexed"
],
"title": "Normalization State",
"type": "string"
},
"source_field": {
"enum": [
"work_identifiers.normalized_value",
"gene_mentions.gene_symbol",
"variant_mentions.normalized_variant",
"phenotype_mentions.hpo_id",
"phenotype_mentions.omim_id",
"phenotype_mentions.mesh_term",
"phenotype_mentions.phenotype_name"
],
"title": "Source Field",
"type": "string"
}
},
"required": [
"entity_type",
"identifier",
"label",
"source_field",
"normalization_state"
],
"title": "PublicCorpusArticleEntity",
"type": "object"
},
"PublicCorpusSearchResult": {
"additionalProperties": false,
"properties": {
"abstract_excerpt": {
"title": "Abstract Excerpt",
"type": "string"
},
"article_entities": {
"items": {
"$ref": "#/$defs/PublicCorpusArticleEntity"
},
"title": "Article Entities",
"type": "array"
},
"authors": {
"items": {
"type": "string"
},
"title": "Authors",
"type": "array"
},
"doi": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Doi"
},
"graph_anchor_pmid": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Graph Anchor Pmid"
},
"graph_score": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"title": "Graph Score"
},
"journal": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Journal"
},
"match_types": {
"items": {
"enum": [
"pmid",
"doi",
"pmcid",
"title",
"abstract",
"gene",
"variant",
"phenotype",
"hpo",
"omim",
"semantic",
"graph"
],
"type": "string"
},
"title": "Match Types",
"type": "array"
},
"pmc_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Pmc Id"
},
"pmid": {
"anyOf": [
{
"pattern": "^[0-9]{1,12}$",
"type": "string"
},
{
"type": "null"
}
],
"title": "Pmid"
},
"publication_date": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Publication Date"
},
"pubmed_url": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Pubmed Url"
},
"rank_score": {
"default": 0,
"title": "Rank Score",
"type": "number"
},
"semantic_score": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"title": "Semantic Score"
},
"source_url": {
"title": "Source Url",
"type": "string"
},
"structured_score": {
"title": "Structured Score",
"type": "number"
},
"title": {
"title": "Title",
"type": "string"
},
"work_id": {
"title": "Work Id",
"type": "string"
}
},
"required": [
"work_id",
"pmid",
"title",
"abstract_excerpt",
"journal",
"publication_date",
"doi",
"pmc_id",
"source_url",
"pubmed_url",
"match_types",
"structured_score"
],
"title": "PublicCorpusSearchResult",
"type": "object"
}
},
"additionalProperties": false,
"properties": {
"contract_version": {
"const": "1.0",
"title": "Contract Version",
"type": "string"
},
"graph_degraded_reason": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Graph Degraded Reason"
},
"graph_used": {
"default": false,
"title": "Graph Used",
"type": "boolean"
},
"graph_version": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Graph Version"
},
"has_more": {
"default": false,
"title": "Has More",
"type": "boolean"
},
"next_cursor": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Next Cursor"
},
"query": {
"title": "Query",
"type": "string"
},
"results": {
"items": {
"$ref": "#/$defs/PublicCorpusSearchResult"
},
"title": "Results",
"type": "array"
},
"returned_count": {
"title": "Returned Count",
"type": "integer"
},
"searchable_fields": {
"items": {
"type": "string"
},
"title": "Searchable Fields",
"type": "array"
},
"semantic_degraded_reason": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Semantic Degraded Reason"
},
"semantic_index_used": {
"default": false,
"title": "Semantic Index Used",
"type": "boolean"
},
"usage_boundary": {
"additionalProperties": true,
"title": "Usage Boundary",
"type": "object"
}
},
"required": [
"contract_version",
"query",
"returned_count",
"results",
"searchable_fields",
"usage_boundary"
],
"title": "PublicCorpusSearchResponse",
"type": "object"
}
},
{
"description": "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.",
"inputSchema": {
"additionalProperties": false,
"description": "The only public scientific input admitted by the MCP tool.",
"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"
],
"title": "SearchVariantArguments",
"type": "object"
},
"name": "search_variant_evidence",
"outputSchema": {
"additionalProperties": false,
"properties": {
"adapter_error": {
"anyOf": [
{
"additionalProperties": false,
"properties": {
"code": {
"minLength": 1,
"type": "string"
},
"message": {
"minLength": 1,
"type": "string"
},
"retryable": {
"type": "boolean"
}
},
"required": [
"code",
"message",
"retryable"
],
"type": "object"
},
{
"type": "null"
}
]
},
"contract_version": {
"const": "1",
"type": "string"
},
"record_url": {
"format": "uri",
"type": [
"string",
"null"
]
},
"result": {
"anyOf": [
{
"additionalProperties": true,
"properties": {
"search_contract_version": {
"const": "1.0",
"type": "string"
},
"status": {
"enum": [
"resolved",
"ambiguous",
"not_found",
"invalid_request",
"unsupported",
"resolution_unavailable"
],
"type": "string"
}
},
"required": [
"search_contract_version",
"status"
],
"type": "object"
},
{
"type": "null"
}
]
},
"usage_boundary": {
"additionalProperties": false,
"properties": {
"intended_use": {
"const": "professional_variant_review",
"type": "string"
},
"not_for": {
"items": {
"enum": [
"patient_diagnosis",
"treatment_decision",
"standalone_clinical_reporting"
],
"type": "string"
},
"maxItems": 3,
"minItems": 3,
"type": "array",
"uniqueItems": true
},
"patient_context_evaluated": {
"const": false,
"type": "boolean"
},
"result_type": {
"const": "automated_variant_level_classification",
"type": "string"
},
"review_required": {
"const": true,
"type": "boolean"
}
},
"required": [
"result_type",
"review_required",
"patient_context_evaluated",
"intended_use",
"not_for"
],
"type": "object"
}
},
"required": [
"contract_version",
"record_url",
"result",
"usage_boundary",
"adapter_error"
],
"type": "object"
}
},
{
"description": "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.",
"inputSchema": {
"additionalProperties": false,
"properties": {
"assembly": {
"const": "GRCh38",
"default": "GRCh38",
"description": "Reference genome assembly. Folklore currently accepts GRCh38 only.",
"title": "Assembly",
"type": "string"
},
"limit": {
"default": 10,
"description": "Maximum number of publications to return, from 1 to 25.",
"maximum": 25,
"minimum": 1,
"title": "Limit",
"type": "integer"
},
"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"
}
},
"required": [
"query"
],
"title": "SearchVariantLiteratureArguments",
"type": "object"
},
"name": "search_variant_literature",
"outputSchema": {
"$defs": {
"CorpusProvenance": {
"additionalProperties": false,
"properties": {
"latest_publication_date": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Latest Publication Date"
},
"publication_count": {
"title": "Publication Count",
"type": "integer"
},
"retrieved_at": {
"title": "Retrieved At",
"type": "string"
},
"semantic_index_used": {
"title": "Semantic Index Used",
"type": "boolean"
},
"source": {
"const": "Helena Literature Corpus canonical works",
"title": "Source",
"type": "string"
}
},
"required": [
"source",
"publication_count",
"latest_publication_date",
"retrieved_at",
"semantic_index_used"
],
"title": "CorpusProvenance",
"type": "object"
},
"LiteratureAuthorityResponse": {
"additionalProperties": false,
"properties": {
"aliases": {
"items": {
"type": "string"
},
"title": "Aliases",
"type": "array"
},
"assembly": {
"const": "GRCh38",
"title": "Assembly",
"type": "string"
},
"candidate_count": {
"title": "Candidate Count",
"type": "integer"
},
"canonical_key": {
"title": "Canonical Key",
"type": "string"
},
"contract_version": {
"const": "1.0",
"title": "Contract Version",
"type": "string"
},
"gene_symbol": {
"title": "Gene Symbol",
"type": "string"
},
"limitations": {
"items": {
"type": "string"
},
"title": "Limitations",
"type": "array"
},
"provenance": {
"$ref": "#/$defs/CorpusProvenance"
},
"publications": {
"items": {
"$ref": "#/$defs/LiteraturePublication"
},
"title": "Publications",
"type": "array"
},
"question": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Question"
}
},
"required": [
"contract_version",
"assembly",
"canonical_key",
"gene_symbol",
"aliases",
"question",
"candidate_count",
"publications",
"provenance",
"limitations"
],
"title": "LiteratureAuthorityResponse",
"type": "object"
},
"LiteraturePublication": {
"additionalProperties": false,
"properties": {
"abstract_excerpt": {
"title": "Abstract Excerpt",
"type": "string"
},
"doi": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Doi"
},
"journal": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Journal"
},
"match_type": {
"enum": [
"exact_variant",
"variant_alias",
"gene_association"
],
"title": "Match Type",
"type": "string"
},
"matched_variant": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Matched Variant"
},
"mention_context": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Mention Context"
},
"phenotype_terms": {
"items": {
"type": "string"
},
"title": "Phenotype Terms",
"type": "array"
},
"pmc_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Pmc Id"
},
"pmid": {
"pattern": "^[0-9]{1,12}$",
"title": "Pmid",
"type": "string"
},
"publication_date": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Publication Date"
},
"pubmed_url": {
"title": "Pubmed Url",
"type": "string"
},
"structured_score": {
"title": "Structured Score",
"type": "number"
},
"title": {
"title": "Title",
"type": "string"
}
},
"required": [
"pmid",
"title",
"abstract_excerpt",
"journal",
"publication_date",
"doi",
"pmc_id",
"pubmed_url",
"match_type",
"matched_variant",
"mention_context",
"phenotype_terms",
"structured_score"
],
"title": "LiteraturePublication",
"type": "object"
}
},
"additionalProperties": false,
"properties": {
"contract_version": {
"const": "1.0",
"default": "1.0",
"title": "Contract Version",
"type": "string"
},
"literature": {
"anyOf": [
{
"$ref": "#/$defs/LiteratureAuthorityResponse"
},
{
"type": "null"
}
]
},
"status": {
"enum": [
"resolved",
"ambiguous",
"not_found",
"invalid_request",
"unsupported",
"resolution_unavailable"
],
"title": "Status",
"type": "string"
},
"usage_boundary": {
"additionalProperties": true,
"title": "Usage Boundary",
"type": "object"
},
"variant_result": {
"additionalProperties": true,
"title": "Variant Result",
"type": "object"
}
},
"required": [
"status",
"variant_result",
"literature",
"usage_boundary"
],
"title": "PublicVariantLiteratureResponse",
"type": "object"
}
},
{
"description": "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.",
"inputSchema": {
"additionalProperties": false,
"properties": {},
"type": "object"
},
"name": "support_helena",
"outputSchema": {
"additionalProperties": true,
"type": "object"
}
}
]
}Verify it yourself
curl -s https://api.teppi.xyz/v1/evidence/sha256:c2216fb6e033d185f5aa23d5aa6c073c1fd6fd4a31abda5b12df23426931946a | sha256sum