Folklore Clinical Variant Interpretation MCP
Bioinformatics MCP for genomic variant interpretation, gene-disease evidence and literature.
Should I use this
Quality & Safety
A
Based on automated analysis of tool definitions and protocol compliance.
Context Cost
~6,721Tokens (tool definitions)
~10.3 KBTypical response size
Significant attention impact (5.25% of 128k context)
This is the approximate number of tokens consumed each time the server's tools are loaded into a model's context. Higher counts reduce the attention available for other tasks.
Install
One-Click Install
Add this to your `claude_desktop_config.json` file:
{
"mcpServers": {
"folklore": {
"url": "https://api.helena.bio/folklore/v1/mcp"
}
}
}Remote endpoints
https://api.helena.bio/folklore/v1/mcpstreamable-httpWhat it can do
Tool inventory
Tools (7)
🟢 Read-only🟡 Write🔴 Delete⚪ Unknown
🟢search_variant_evidence(assembly, query)
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.
Input 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"
}Output Schema
{
"type": "object",
"properties": {
"contract_version": {
"type": "string",
"const": "1"
},
"record_url": {
"type": [
"string",
"null"
],
"format": "uri"
},
"result": {
"anyOf": [
{
"type": "object",
"required": [
"search_contract_version",
"status"
],
"properties": {
"search_contract_version": {
"type": "string",
"const": "1.0"
},
"status": {
"type": "string",
"enum": [
"resolved",
"ambiguous",
"not_found",
"invalid_request",
"unsupported",
"resolution_unavailable"
]
}
},
"additionalProperties": true
},
{
"type": "null"
}
]
},
"usage_boundary": {
"type": "object",
"additionalProperties": false,
"required": [
"result_type",
"review_required",
"patient_context_evaluated",
"intended_use",
"not_for"
],
"properties": {
"result_type": {
"type": "string",
"const": "automated_variant_level_classification"
},
"review_required": {
"type": "boolean",
"const": true
},
"patient_context_evaluated": {
"type": "boolean",
"const": false
},
"intended_use": {
"type": "string",
"const": "professional_variant_review"
},
"not_for": {
"type": "array",
"items": {
"type": "string",
"enum": [
"patient_diagnosis",
"treatment_decision",
"standalone_clinical_reporting"
]
},
"minItems": 3,
"maxItems": 3,
"uniqueItems": true
}
}
},
"adapter_error": {
"anyOf": [
{
"type": "object",
"additionalProperties": false,
"required": [
"code",
"message",
"retryable"
],
"properties": {
"code": {
"type": "string",
"minLength": 1
},
"message": {
"type": "string",
"minLength": 1
},
"retryable": {
"type": "boolean"
}
}
},
{
"type": "null"
}
]
}
},
"required": [
"contract_version",
"record_url",
"result",
"usage_boundary",
"adapter_error"
],
"additionalProperties": false
}🟢search_variant_literature(assembly, query, question, limit)
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.
Input 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"
}Output Schema
{
"type": "object",
"properties": {
"contract_version": {
"const": "1.0",
"default": "1.0",
"title": "Contract Version",
"type": "string"
},
"status": {
"enum": [
"resolved",
"ambiguous",
"not_found",
"invalid_request",
"unsupported",
"resolution_unavailable"
],
"title": "Status",
"type": "string"
},
"variant_result": {
"additionalProperties": true,
"title": "Variant Result",
"type": "object"
},
"literature": {
"anyOf": [
{
"$ref": "#/$defs/LiteratureAuthorityResponse"
},
{
"type": "null"
}
]
},
"usage_boundary": {
"additionalProperties": true,
"title": "Usage Boundary",
"type": "object"
}
},
"required": [
"status",
"variant_result",
"literature",
"usage_boundary"
],
"$defs": {
"CorpusProvenance": {
"additionalProperties": false,
"properties": {
"source": {
"const": "Helena Literature Corpus canonical works",
"title": "Source",
"type": "string"
},
"publication_count": {
"title": "Publication Count",
"type": "integer"
},
"latest_publication_date": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Latest Publication Date"
},
"retrieved_at": {
"title": "Retrieved At",
"type": "string"
},
"semantic_index_used": {
"title": "Semantic Index Used",
"type": "boolean"
}
},
"required": [
"source",
"publication_count",
"latest_publication_date",
"retrieved_at",
"semantic_index_used"
],
"title": "CorpusProvenance",
"type": "object"
},
"LiteratureAuthorityResponse": {
"additionalProperties": false,
"properties": {
"contract_version": {
"const": "1.0",
"title": "Contract Version",
"type": "string"
},
"assembly": {
"const": "GRCh38",
"title": "Assembly",
"type": "string"
},
"canonical_key": {
"title": "Canonical Key",
"type": "string"
},
"gene_symbol": {
"title": "Gene Symbol",
"type": "string"
},
"aliases": {
"items": {
"type": "string"
},
"title": "Aliases",
"type": "array"
},
"question": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Question"
},
"candidate_count": {
"title": "Candidate Count",
"type": "integer"
},
"publications": {
"items": {
"$ref": "#/$defs/LiteraturePublication"
},
"title": "Publications",
"type": "array"
},
"provenance": {
"$ref": "#/$defs/CorpusProvenance"
},
"limitations": {
"items": {
"type": "string"
},
"title": "Limitations",
"type": "array"
}
},
"required": [
"contract_version",
"assembly",
"canonical_key",
"gene_symbol",
"aliases",
"question",
"candidate_count",
"publications",
"provenance",
"limitations"
],
"title": "LiteratureAuthorityResponse",
"type": "object"
},
"LiteraturePublication": {
"additionalProperties": false,
"properties": {
"pmid": {
"pattern": "^[0-9]{1,12}$",
"title": "Pmid",
"type": "string"
},
"title": {
"title": "Title",
"type": "string"
},
"abstract_excerpt": {
"title": "Abstract Excerpt",
"type": "string"
},
"journal": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Journal"
},
"publication_date": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Publication Date"
},
"doi": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Doi"
},
"pmc_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Pmc Id"
},
"pubmed_url": {
"title": "Pubmed Url",
"type": "string"
},
"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"
},
"structured_score": {
"title": "Structured Score",
"type": "number"
}
},
"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,
"title": "PublicVariantLiteratureResponse"
}🟢get_publication_details(pmid)
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.
Input 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}$",
"title": "Pmid",
"type": "string"
}
},
"required": [
"pmid"
],
"additionalProperties": false,
"title": "GetPublicationDetailsArguments"
}Output Schema
{
"type": "object",
"properties": {
"contract_version": {
"const": "1.0",
"title": "Contract Version",
"type": "string"
},
"publication": {
"$ref": "#/$defs/PublicPublicationDetails"
},
"usage_boundary": {
"additionalProperties": true,
"title": "Usage Boundary",
"type": "object"
}
},
"required": [
"contract_version",
"publication",
"usage_boundary"
],
"$defs": {
"PublicAbstractReuse": {
"additionalProperties": false,
"properties": {
"allowed": {
"default": false,
"title": "Allowed",
"type": "boolean"
},
"license": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "License"
},
"evidence_url": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Evidence Url"
},
"source": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Source"
}
},
"title": "PublicAbstractReuse",
"type": "object"
},
"PublicGeneMention": {
"additionalProperties": false,
"properties": {
"gene_symbol": {
"title": "Gene Symbol",
"type": "string"
},
"association_type": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Association Type"
},
"mention_count": {
"title": "Mention Count",
"type": "integer"
}
},
"required": [
"gene_symbol",
"association_type",
"mention_count"
],
"title": "PublicGeneMention",
"type": "object"
},
"PublicPublicationDetails": {
"additionalProperties": false,
"properties": {
"pmid": {
"pattern": "^[0-9]{1,12}$",
"title": "Pmid",
"type": "string"
},
"title": {
"title": "Title",
"type": "string"
},
"abstract": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Abstract"
},
"authors": {
"items": {
"type": "string"
},
"title": "Authors",
"type": "array"
},
"journal": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Journal"
},
"publication_date": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Publication Date"
},
"publication_types": {
"items": {
"type": "string"
},
"title": "Publication Types",
"type": "array"
},
"mesh_terms": {
"items": {
"type": "string"
},
"title": "Mesh Terms",
"type": "array"
},
"doi": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Doi"
},
"pmc_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Pmc Id"
},
"is_retracted": {
"title": "Is Retracted",
"type": "boolean"
},
"pubmed_url": {
"title": "Pubmed Url",
"type": "string"
},
"full_text_url": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Full Text Url"
},
"abstract_reuse": {
"$ref": "#/$defs/PublicAbstractReuse"
},
"gene_mentions": {
"items": {
"$ref": "#/$defs/PublicGeneMention"
},
"title": "Gene Mentions",
"type": "array"
},
"variant_mentions": {
"items": {
"$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": {
"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"
},
"clinical_significance": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Clinical Significance"
},
"evidence_type": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Evidence Type"
},
"sentence_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Sentence Text"
},
"confidence_score": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"title": "Confidence Score"
}
},
"required": [
"gene_symbol",
"hgvs_cdna",
"hgvs_protein",
"normalized_variant",
"clinical_significance",
"evidence_type",
"sentence_text",
"confidence_score"
],
"title": "PublicVariantMention",
"type": "object"
}
},
"additionalProperties": false,
"title": "PublicationDetailsResponse"
}🟢search_literature_corpus(query, limit, sort, cursor)
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.
Input 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"
}Output Schema
{
"type": "object",
"properties": {
"contract_version": {
"const": "1.0",
"title": "Contract Version",
"type": "string"
},
"query": {
"title": "Query",
"type": "string"
},
"returned_count": {
"title": "Returned Count",
"type": "integer"
},
"results": {
"items": {
"$ref": "#/$defs/PublicCorpusSearchResult"
},
"title": "Results",
"type": "array"
},
"has_more": {
"default": false,
"title": "Has More",
"type": "boolean"
},
"next_cursor": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Next Cursor"
},
"searchable_fields": {
"items": {
"type": "string"
},
"title": "Searchable Fields",
"type": "array"
},
"semantic_index_used": {
"default": false,
"title": "Semantic Index Used",
"type": "boolean"
},
"semantic_degraded_reason": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Semantic Degraded Reason"
},
"graph_used": {
"default": false,
"title": "Graph Used",
"type": "boolean"
},
"graph_version": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Graph Version"
},
"graph_degraded_reason": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Graph Degraded Reason"
},
"usage_boundary": {
"additionalProperties": true,
"title": "Usage Boundary",
"type": "object"
}
},
"required": [
"contract_version",
"query",
"returned_count",
"results",
"searchable_fields",
"usage_boundary"
],
"$defs": {
"PublicCorpusArticleEntity": {
"additionalProperties": false,
"properties": {
"entity_type": {
"enum": [
"gene",
"variant",
"phenotype",
"pmid",
"doi",
"pmcid",
"omim"
],
"title": "Entity Type",
"type": "string"
},
"identifier": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Identifier"
},
"label": {
"title": "Label",
"type": "string"
},
"source_field": {
"enum": [
"work_identifiers.normalized_value",
"gene_mentions.gene_symbol",
"variant_mentions.normalized_variant",
"phenotype_mentions.hpo_id",
"phenotype_mentions.omim_id",
"phenotype_mentions.mesh_term",
"phenotype_mentions.phenotype_name"
],
"title": "Source Field",
"type": "string"
},
"normalization_state": {
"enum": [
"normalized",
"source_indexed"
],
"title": "Normalization State",
"type": "string"
}
},
"required": [
"entity_type",
"identifier",
"label",
"source_field",
"normalization_state"
],
"title": "PublicCorpusArticleEntity",
"type": "object"
},
"PublicCorpusSearchResult": {
"additionalProperties": false,
"properties": {
"work_id": {
"title": "Work Id",
"type": "string"
},
"pmid": {
"anyOf": [
{
"pattern": "^[0-9]{1,12}$",
"type": "string"
},
{
"type": "null"
}
],
"title": "Pmid"
},
"title": {
"title": "Title",
"type": "string"
},
"abstract_excerpt": {
"title": "Abstract Excerpt",
"type": "string"
},
"authors": {
"items": {
"type": "string"
},
"title": "Authors",
"type": "array"
},
"journal": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Journal"
},
"publication_date": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Publication Date"
},
"doi": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Doi"
},
"pmc_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Pmc Id"
},
"source_url": {
"title": "Source Url",
"type": "string"
},
"pubmed_url": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Pubmed Url"
},
"match_types": {
"items": {
"enum": [
"pmid",
"doi",
"pmcid",
"title",
"abstract",
"gene",
"variant",
"phenotype",
"hpo",
"omim",
"semantic",
"graph"
],
"type": "string"
},
"title": "Match Types",
"type": "array"
},
"structured_score": {
"title": "Structured Score",
"type": "number"
},
"semantic_score": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"title": "Semantic Score"
},
"graph_score": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"title": "Graph Score"
},
"graph_anchor_pmid": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Graph Anchor Pmid"
},
"rank_score": {
"default": 0,
"title": "Rank Score",
"type": "number"
},
"article_entities": {
"items": {
"$ref": "#/$defs/PublicCorpusArticleEntity"
},
"title": "Article Entities",
"type": "array"
}
},
"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,
"title": "PublicCorpusSearchResponse"
}🟢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.
Input Schema
{
"type": "object",
"properties": {},
"additionalProperties": false
}Output Schema
{
"type": "object",
"additionalProperties": true
}🟢get_gene_disease_associations(limit, offset, gene)
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.
Input 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"
}Output Schema
{
"type": "object",
"properties": {
"contractVersion": {
"const": "1.0",
"title": "Contractversion",
"type": "string"
},
"status": {
"enum": [
"ok",
"not_found"
],
"title": "Status",
"type": "string"
},
"query": {
"$ref": "#/$defs/Query"
},
"associations": {
"items": {
"$ref": "#/$defs/Association"
},
"maxItems": 50,
"title": "Associations",
"type": "array"
},
"pagination": {
"$ref": "#/$defs/Pagination"
},
"source": {
"$ref": "#/$defs/Source"
},
"warnings": {
"items": {
"type": "string"
},
"title": "Warnings",
"type": "array"
},
"usage_boundary": {
"$ref": "#/$defs/UsageBoundary"
}
},
"required": [
"contractVersion",
"status",
"query",
"associations",
"pagination",
"source",
"warnings",
"usage_boundary"
],
"$defs": {
"Association": {
"additionalProperties": false,
"properties": {
"geneSymbol": {
"title": "Genesymbol",
"type": "string"
},
"hgncId": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Hgncid"
},
"diseaseName": {
"title": "Diseasename",
"type": "string"
},
"diseaseId": {
"title": "Diseaseid",
"type": "string"
},
"modeOfInheritance": {
"title": "Modeofinheritance",
"type": "string"
},
"modeOfInheritanceId": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Modeofinheritanceid"
},
"classification": {
"title": "Classification",
"type": "string"
},
"expertPanel": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Expertpanel"
},
"reportUrl": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Reporturl"
},
"classificationDate": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Classificationdate"
},
"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"
},
"offset": {
"maximum": 1000,
"minimum": 0,
"title": "Offset",
"type": "integer"
},
"total": {
"minimum": 0,
"title": "Total",
"type": "integer"
},
"nextOffset": {
"anyOf": [
{
"maximum": 1000,
"minimum": 0,
"type": "integer"
},
{
"type": "null"
}
],
"title": "Nextoffset"
}
},
"required": [
"limit",
"offset",
"total",
"nextOffset"
],
"title": "Pagination",
"type": "object"
},
"Query": {
"additionalProperties": false,
"properties": {
"kind": {
"enum": [
"gene",
"disease"
],
"title": "Kind",
"type": "string"
},
"value": {
"title": "Value",
"type": "string"
},
"match": {
"enum": [
"exact",
"name_contains"
],
"title": "Match",
"type": "string"
}
},
"required": [
"kind",
"value",
"match"
],
"title": "Query",
"type": "object"
},
"Source": {
"additionalProperties": false,
"properties": {
"name": {
"const": "ClinGen Gene-Disease Validity",
"title": "Name",
"type": "string"
},
"version": {
"title": "Version",
"type": "string"
},
"snapshotSha256": {
"pattern": "^[a-f0-9]{64}$",
"title": "Snapshotsha256",
"type": "string"
},
"downloadUrl": {
"title": "Downloadurl",
"type": "string"
},
"license": {
"const": "CC0-1.0",
"title": "License",
"type": "string"
},
"attribution": {
"title": "Attribution",
"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"
},
"patient_context_evaluated": {
"const": false,
"title": "Patient Context Evaluated",
"type": "boolean"
},
"review_required": {
"const": true,
"title": "Review Required",
"type": "boolean"
},
"not_for": {
"items": {
"enum": [
"patient_diagnosis",
"treatment_decision",
"variant_pathogenicity_classification"
],
"type": "string"
},
"title": "Not For",
"type": "array"
}
},
"required": [
"intended_use",
"patient_context_evaluated",
"review_required",
"not_for"
],
"title": "UsageBoundary",
"type": "object"
}
},
"additionalProperties": false,
"title": "GeneDiseaseResponse"
}🟢search_disease_genes(limit, offset, disease)
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.
Input 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"
}Output Schema
{
"type": "object",
"properties": {
"contractVersion": {
"const": "1.0",
"title": "Contractversion",
"type": "string"
},
"status": {
"enum": [
"ok",
"not_found"
],
"title": "Status",
"type": "string"
},
"query": {
"$ref": "#/$defs/Query"
},
"associations": {
"items": {
"$ref": "#/$defs/Association"
},
"maxItems": 50,
"title": "Associations",
"type": "array"
},
"pagination": {
"$ref": "#/$defs/Pagination"
},
"source": {
"$ref": "#/$defs/Source"
},
"warnings": {
"items": {
"type": "string"
},
"title": "Warnings",
"type": "array"
},
"usage_boundary": {
"$ref": "#/$defs/UsageBoundary"
}
},
"required": [
"contractVersion",
"status",
"query",
"associations",
"pagination",
"source",
"warnings",
"usage_boundary"
],
"$defs": {
"Association": {
"additionalProperties": false,
"properties": {
"geneSymbol": {
"title": "Genesymbol",
"type": "string"
},
"hgncId": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Hgncid"
},
"diseaseName": {
"title": "Diseasename",
"type": "string"
},
"diseaseId": {
"title": "Diseaseid",
"type": "string"
},
"modeOfInheritance": {
"title": "Modeofinheritance",
"type": "string"
},
"modeOfInheritanceId": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Modeofinheritanceid"
},
"classification": {
"title": "Classification",
"type": "string"
},
"expertPanel": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Expertpanel"
},
"reportUrl": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Reporturl"
},
"classificationDate": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Classificationdate"
},
"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"
},
"offset": {
"maximum": 1000,
"minimum": 0,
"title": "Offset",
"type": "integer"
},
"total": {
"minimum": 0,
"title": "Total",
"type": "integer"
},
"nextOffset": {
"anyOf": [
{
"maximum": 1000,
"minimum": 0,
"type": "integer"
},
{
"type": "null"
}
],
"title": "Nextoffset"
}
},
"required": [
"limit",
"offset",
"total",
"nextOffset"
],
"title": "Pagination",
"type": "object"
},
"Query": {
"additionalProperties": false,
"properties": {
"kind": {
"enum": [
"gene",
"disease"
],
"title": "Kind",
"type": "string"
},
"value": {
"title": "Value",
"type": "string"
},
"match": {
"enum": [
"exact",
"name_contains"
],
"title": "Match",
"type": "string"
}
},
"required": [
"kind",
"value",
"match"
],
"title": "Query",
"type": "object"
},
"Source": {
"additionalProperties": false,
"properties": {
"name": {
"const": "ClinGen Gene-Disease Validity",
"title": "Name",
"type": "string"
},
"version": {
"title": "Version",
"type": "string"
},
"snapshotSha256": {
"pattern": "^[a-f0-9]{64}$",
"title": "Snapshotsha256",
"type": "string"
},
"downloadUrl": {
"title": "Downloadurl",
"type": "string"
},
"license": {
"const": "CC0-1.0",
"title": "License",
"type": "string"
},
"attribution": {
"title": "Attribution",
"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"
},
"patient_context_evaluated": {
"const": false,
"title": "Patient Context Evaluated",
"type": "boolean"
},
"review_required": {
"const": true,
"title": "Review Required",
"type": "boolean"
},
"not_for": {
"items": {
"enum": [
"patient_diagnosis",
"treatment_decision",
"variant_pathogenicity_classification"
],
"type": "string"
},
"title": "Not For",
"type": "array"
}
},
"required": [
"intended_use",
"patient_context_evaluated",
"review_required",
"not_for"
],
"title": "UsageBoundary",
"type": "object"
}
},
"additionalProperties": false,
"title": "GeneDiseaseResponse"
}Community
Evidence
Recent observations
verifiedversion not recorded7 tools
verifiedversion not recorded7 tools