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MCP Server

Folklore Clinical Variant Interpretation MCP

io.github.helena-bioinformatics/folklore
Healthcare Science & Engineering Search & Research Public & reachable MCP 2025-11-25

What this MCP does

Supports clinical genomics research through gene-disease associations, germline variant interpretation, biomedical literature search, and publication details.

Capabilities

Tools

7 tools
get_gene_disease_associations
Find diseases associated with a 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.
Read only Idempotent
Input schema 
{'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}
Output schema 
{'type': 'object', '$defs': {'Query': {'type': 'object', 'title': 'Query', 'required': ['kind', 'value', 'match'], 'properties': {'kind': {'enum': ['gene', 'disease'], 'type': 'string', 'title': 'Kind'}, 'match': {'enum': ['exact', 'name_contains'], 'type': 'string', 'title': 'Match'}, 'value': {'type': 'string', 'title': 'Value'}}, 'additionalProperties': False}, 'Source': {'type': 'object', 'title': 'Source', 'required': ['name', 'version', 'snapshotSha256', 'downloadUrl', 'license', 'attribution'], 'properties': {'name': {'type': 'string', 'const': 'ClinGen Gene-Disease Validity', 'title': 'Name'}, 'license': {'type': 'string', 'const': 'CC0-1.0', 'title': 'License'}, 'version': {'type': 'string', 'title': 'Version'}, 'attribution': {'type': 'string', 'title': 'Attribution'}, 'downloadUrl': {'type': 'string', 'title': 'Downloadurl'}, 'snapshotSha256': {'type': 'string', 'title': 'Snapshotsha256', 'pattern': '^[a-f0-9]{64}$'}}, 'additionalProperties': False}, 'Pagination': {'type': 'object', 'title': 'Pagination', 'required': ['limit', 'offset', 'total', 'nextOffset'], 'properties': {'limit': {'type': 'integer', 'title': 'Limit', 'maximum': 50, 'minimum': 1}, 'total': {'type': 'integer', 'title': 'Total', 'minimum': 0}, 'offset': {'type': 'integer', 'title': 'Offset', 'maximum': 1000, 'minimum': 0}, 'nextOffset': {'anyOf': [{'type': 'integer', 'maximum': 1000, 'minimum': 0}, {'type': 'null'}], 'title': 'Nextoffset'}}, 'additionalProperties': False}, 'Association': {'type': 'object', 'title': 'Association', 'required': ['geneSymbol', 'hgncId', 'diseaseName', 'diseaseId', 'modeOfInheritance', 'modeOfInheritanceId', 'classification', 'expertPanel', 'reportUrl', 'classificationDate', 'sopVersion'], 'properties': {'hgncId': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Hgncid'}, 'diseaseId': {'type': 'string', 'title': 'Diseaseid'}, 'reportUrl': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Reporturl'}, 'geneSymbol': {'type': 'string', 'title': 'Genesymbol'}, 'sopVersion': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Sopversion'}, 'diseaseName': {'type': 'string', 'title': 'Diseasename'}, 'expertPanel': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Expertpanel'}, 'classification': {'type': 'string', 'title': 'Classification'}, 'modeOfInheritance': {'type': 'string', 'title': 'Modeofinheritance'}, 'classificationDate': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Classificationdate'}, 'modeOfInheritanceId': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Modeofinheritanceid'}}, 'additionalProperties': False}, 'UsageBoundary': {'type': 'object', 'title': 'UsageBoundary', 'required': ['intended_use', 'patient_context_evaluated', 'review_required', 'not_for'], 'properties': {'not_for': {'type': 'array', 'items': {'enum': ['patient_diagnosis', 'treatment_decision', 'variant_pathogenicity_classification'], 'type': 'string'}, 'title': 'Not For'}, 'intended_use': {'type': 'string', 'const': 'professional_gene_disease_review', 'title': 'Intended Use'}, 'review_required': {'type': 'boolean', 'const': True, 'title': 'Review Required'}, 'patient_context_evaluated': {'type': 'boolean', 'const': False, 'title': 'Patient Context Evaluated'}}, 'additionalProperties': False}}, 'title': 'GeneDiseaseResponse', 'required': ['contractVersion', 'status', 'query', 'associations', 'pagination', 'source', 'warnings', 'usage_boundary'], 'properties': {'query': {'$ref': '#/$defs/Query'}, 'source': {'$ref': '#/$defs/Source'}, 'status': {'enum': ['ok', 'not_found'], 'type': 'string', 'title': 'Status'}, 'warnings': {'type': 'array', 'items': {'type': 'string'}, 'title': 'Warnings'}, 'pagination': {'$ref': '#/$defs/Pagination'}, 'associations': {'type': 'array', 'items': {'$ref': '#/$defs/Association'}, 'title': 'Associations', 'maxItems': 50}, 'usage_boundary': {'$ref': '#/$defs/UsageBoundary'}, 'contractVersion': {'type': 'string', 'const': '1.0', 'title': 'Contractversion'}}, 'additionalProperties': False}
get_publication_details
Get details for a PubMed publication
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 Idempotent
Input schema 
{'type': 'object', 'title': 'GetPublicationDetailsArguments', 'required': ['pmid'], 'properties': {'pmid': {'type': 'string', 'title': 'Pmid', 'pattern': '^[0-9]{1,12}$', 'description': "One PubMed identifier to look up in Folklore's current corpus, as 1 to 12 digits without a PMID prefix."}}, 'additionalProperties': False}
Output schema 
{'type': 'object', '$defs': {'PublicGeneMention': {'type': 'object', 'title': 'PublicGeneMention', 'required': ['gene_symbol', 'association_type', 'mention_count'], 'properties': {'gene_symbol': {'type': 'string', 'title': 'Gene Symbol'}, 'mention_count': {'type': 'integer', 'title': 'Mention Count'}, 'association_type': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Association Type'}}, 'additionalProperties': False}, 'PublicAbstractReuse': {'type': 'object', 'title': 'PublicAbstractReuse', 'properties': {'source': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Source', 'default': None}, 'allowed': {'type': 'boolean', 'title': 'Allowed', 'default': False}, 'license': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'License', 'default': None}, 'evidence_url': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Evidence Url', 'default': None}}, 'additionalProperties': False}, 'PublicVariantMention': {'type': 'object', 'title': 'PublicVariantMention', 'required': ['gene_symbol', 'hgvs_cdna', 'hgvs_protein', 'normalized_variant', 'clinical_significance', 'evidence_type', 'sentence_text', 'confidence_score'], 'properties': {'hgvs_cdna': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Hgvs Cdna'}, 'gene_symbol': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Gene Symbol'}, 'hgvs_protein': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Hgvs Protein'}, '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'}, 'normalized_variant': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Normalized Variant'}, 'clinical_significance': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Clinical Significance'}}, 'additionalProperties': False}, 'PublicPublicationDetails': {'type': 'object', 'title': 'PublicPublicationDetails', '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'], 'properties': {'doi': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Doi'}, 'pmid': {'type': 'string', 'title': 'Pmid', 'pattern': '^[0-9]{1,12}$'}, 'title': {'type': 'string', 'title': 'Title'}, 'pmc_id': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Pmc Id'}, 'authors': {'type': 'array', 'items': {'type': 'string'}, 'title': 'Authors'}, 'journal': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Journal'}, 'abstract': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Abstract'}, 'mesh_terms': {'type': 'array', 'items': {'type': 'string'}, 'title': 'Mesh Terms'}, 'pubmed_url': {'type': 'string', 'title': 'Pubmed Url'}, 'is_retracted': {'type': 'boolean', 'title': 'Is Retracted'}, 'full_text_url': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Full Text Url'}, 'gene_mentions': {'type': 'array', 'items': {'$ref': '#/$defs/PublicGeneMention'}, 'title': 'Gene Mentions'}, 'abstract_reuse': {'$ref': '#/$defs/PublicAbstractReuse'}, 'publication_date': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Publication Date'}, 'variant_mentions': {'type': 'array', 'items': {'$ref': '#/$defs/PublicVariantMention'}, 'title': 'Variant Mentions'}, 'publication_types': {'type': 'array', 'items': {'type': 'string'}, 'title': 'Publication Types'}}, 'additionalProperties': False}}, 'title': 'PublicationDetailsResponse', 'required': ['contract_version', 'publication', 'usage_boundary'], 'properties': {'publication': {'$ref': '#/$defs/PublicPublicationDetails'}, 'usage_boundary': {'type': 'object', 'title': 'Usage Boundary', 'additionalProperties': True}, 'contract_version': {'type': 'string', 'const': '1.0', 'title': 'Contract Version'}}, 'additionalProperties': False}
search_disease_genes
Find genes associated with a disease
Find human genes associated with a disease for genomic analysis and rare-disease research. Accepts an exact MONDO identifier or a disease-name search. Returns matching ClinGen gene-disease validity assertions with inheritance, source reports and snapshot provenance. Name searches may match multiple diseases; preserve their distinct identities and do not infer a diagnosis. Use only a public disease name or identifier; no symptoms, patient or case data. Results require professional review.
Read only Idempotent
Input schema 
{'type': 'object', 'title': 'SearchDiseaseGenesArguments', 'required': ['disease'], 'properties': {'limit': {'type': 'integer', 'title': 'Limit', 'default': 20, 'maximum': 50, 'minimum': 1, 'description': 'Maximum number of source assertions per page, from 1 to 50.'}, 'offset': {'type': 'integer', 'title': 'Offset', 'default': 0, 'maximum': 1000, 'minimum': 0, 'description': 'Zero-based assertion offset; use the returned nextOffset when present.'}, 'disease': {'type': 'string', 'title': 'Disease', 'maxLength': 160, 'minLength': 3, 'description': 'One public disease name or exact MONDO identifier (MONDO: followed by seven digits). A name search may match multiple distinct diseases. No symptoms or patient narrative.'}}, 'additionalProperties': False}
Output schema 
{'type': 'object', '$defs': {'Query': {'type': 'object', 'title': 'Query', 'required': ['kind', 'value', 'match'], 'properties': {'kind': {'enum': ['gene', 'disease'], 'type': 'string', 'title': 'Kind'}, 'match': {'enum': ['exact', 'name_contains'], 'type': 'string', 'title': 'Match'}, 'value': {'type': 'string', 'title': 'Value'}}, 'additionalProperties': False}, 'Source': {'type': 'object', 'title': 'Source', 'required': ['name', 'version', 'snapshotSha256', 'downloadUrl', 'license', 'attribution'], 'properties': {'name': {'type': 'string', 'const': 'ClinGen Gene-Disease Validity', 'title': 'Name'}, 'license': {'type': 'string', 'const': 'CC0-1.0', 'title': 'License'}, 'version': {'type': 'string', 'title': 'Version'}, 'attribution': {'type': 'string', 'title': 'Attribution'}, 'downloadUrl': {'type': 'string', 'title': 'Downloadurl'}, 'snapshotSha256': {'type': 'string', 'title': 'Snapshotsha256', 'pattern': '^[a-f0-9]{64}$'}}, 'additionalProperties': False}, 'Pagination': {'type': 'object', 'title': 'Pagination', 'required': ['limit', 'offset', 'total', 'nextOffset'], 'properties': {'limit': {'type': 'integer', 'title': 'Limit', 'maximum': 50, 'minimum': 1}, 'total': {'type': 'integer', 'title': 'Total', 'minimum': 0}, 'offset': {'type': 'integer', 'title': 'Offset', 'maximum': 1000, 'minimum': 0}, 'nextOffset': {'anyOf': [{'type': 'integer', 'maximum': 1000, 'minimum': 0}, {'type': 'null'}], 'title': 'Nextoffset'}}, 'additionalProperties': False}, 'Association': {'type': 'object', 'title': 'Association', 'required': ['geneSymbol', 'hgncId', 'diseaseName', 'diseaseId', 'modeOfInheritance', 'modeOfInheritanceId', 'classification', 'expertPanel', 'reportUrl', 'classificationDate', 'sopVersion'], 'properties': {'hgncId': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Hgncid'}, 'diseaseId': {'type': 'string', 'title': 'Diseaseid'}, 'reportUrl': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Reporturl'}, 'geneSymbol': {'type': 'string', 'title': 'Genesymbol'}, 'sopVersion': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Sopversion'}, 'diseaseName': {'type': 'string', 'title': 'Diseasename'}, 'expertPanel': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Expertpanel'}, 'classification': {'type': 'string', 'title': 'Classification'}, 'modeOfInheritance': {'type': 'string', 'title': 'Modeofinheritance'}, 'classificationDate': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Classificationdate'}, 'modeOfInheritanceId': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Modeofinheritanceid'}}, 'additionalProperties': False}, 'UsageBoundary': {'type': 'object', 'title': 'UsageBoundary', 'required': ['intended_use', 'patient_context_evaluated', 'review_required', 'not_for'], 'properties': {'not_for': {'type': 'array', 'items': {'enum': ['patient_diagnosis', 'treatment_decision', 'variant_pathogenicity_classification'], 'type': 'string'}, 'title': 'Not For'}, 'intended_use': {'type': 'string', 'const': 'professional_gene_disease_review', 'title': 'Intended Use'}, 'review_required': {'type': 'boolean', 'const': True, 'title': 'Review Required'}, 'patient_context_evaluated': {'type': 'boolean', 'const': False, 'title': 'Patient Context Evaluated'}}, 'additionalProperties': False}}, 'title': 'GeneDiseaseResponse', 'required': ['contractVersion', 'status', 'query', 'associations', 'pagination', 'source', 'warnings', 'usage_boundary'], 'properties': {'query': {'$ref': '#/$defs/Query'}, 'source': {'$ref': '#/$defs/Source'}, 'status': {'enum': ['ok', 'not_found'], 'type': 'string', 'title': 'Status'}, 'warnings': {'type': 'array', 'items': {'type': 'string'}, 'title': 'Warnings'}, 'pagination': {'$ref': '#/$defs/Pagination'}, 'associations': {'type': 'array', 'items': {'$ref': '#/$defs/Association'}, 'title': 'Associations', 'maxItems': 50}, 'usage_boundary': {'$ref': '#/$defs/UsageBoundary'}, 'contractVersion': {'type': 'string', 'const': '1.0', 'title': 'Contractversion'}}, 'additionalProperties': False}
search_literature_corpus
Search the Folklore Literature Corpus
Semantically search the public scientific Literature Corpus by a natural-language question. A question may include one or more PMID, DOI or PMCID references; those publications become exact anchors for finding related experiments, evidence and concepts across the corpus. Also accepts genes, variants, phenotypes, HPO and OMIM concepts. Include every known publication identifier in the query when the user asks to compare papers or find work related to a specific paper. Returns source-linked evidence candidates for professional review, not diagnoses, causality claims or treatment recommendations.
Read only Idempotent
Input schema 
{'type': 'object', 'title': 'SearchCorpusArguments', 'required': ['query'], 'properties': {'sort': {'enum': ['relevance', 'newest', 'oldest'], 'type': 'string', 'title': 'Sort', 'default': 'relevance', 'description': 'Result ordering: relevance-ranked, newest publication first, or oldest publication first.'}, 'limit': {'type': 'integer', 'title': 'Limit', 'default': 20, 'maximum': 25, 'minimum': 1, 'description': 'Maximum number of publications to return, from 1 to 25.'}, 'query': {'type': 'string', 'title': 'Query', 'maxLength': 200, 'minLength': 3, 'description': 'Natural-language literature question or exact PMID, DOI, PMCID, gene, variant, phenotype, HPO, or OMIM query. Include every known publication identifier when comparing or finding related papers.'}, 'cursor': {'anyOf': [{'type': 'string', 'pattern': '^[A-Za-z0-9_-]+$', 'maxLength': 128, 'minLength': 8}, {'type': 'null'}], 'title': 'Cursor', 'default': None, 'description': 'Opaque continuation cursor from the preceding response for the same query and sort order; omit for the first page.'}}, 'additionalProperties': False}
Output schema 
{'type': 'object', '$defs': {'PublicCorpusSearchResult': {'type': 'object', 'title': 'PublicCorpusSearchResult', 'required': ['work_id', 'pmid', 'title', 'abstract_excerpt', 'journal', 'publication_date', 'doi', 'pmc_id', 'source_url', 'pubmed_url', 'match_types', 'structured_score'], 'properties': {'doi': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Doi'}, 'pmid': {'anyOf': [{'type': 'string', 'pattern': '^[0-9]{1,12}$'}, {'type': 'null'}], 'title': 'Pmid'}, 'title': {'type': 'string', 'title': 'Title'}, 'pmc_id': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Pmc Id'}, 'authors': {'type': 'array', 'items': {'type': 'string'}, 'title': 'Authors'}, 'journal': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Journal'}, 'work_id': {'type': 'string', 'title': 'Work Id'}, 'pubmed_url': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Pubmed Url'}, 'rank_score': {'type': 'number', 'title': 'Rank Score', 'default': 0.0}, 'source_url': {'type': 'string', 'title': 'Source Url'}, 'graph_score': {'anyOf': [{'type': 'number'}, {'type': 'null'}], 'title': 'Graph Score', 'default': None}, 'match_types': {'type': 'array', 'items': {'enum': ['pmid', 'doi', 'pmcid', 'title', 'abstract', 'gene', 'variant', 'phenotype', 'hpo', 'omim', 'semantic', 'graph'], 'type': 'string'}, 'title': 'Match Types'}, 'semantic_score': {'anyOf': [{'type': 'number'}, {'type': 'null'}], 'title': 'Semantic Score', 'default': None}, 'abstract_excerpt': {'type': 'string', 'title': 'Abstract Excerpt'}, 'article_entities': {'type': 'array', 'items': {'$ref': '#/$defs/PublicCorpusArticleEntity'}, 'title': 'Article Entities'}, 'publication_date': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Publication Date'}, 'structured_score': {'type': 'number', 'title': 'Structured Score'}, 'graph_anchor_pmid': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Graph Anchor Pmid', 'default': None}}, 'additionalProperties': False}, 'PublicCorpusArticleEntity': {'type': 'object', 'title': 'PublicCorpusArticleEntity', 'required': ['entity_type', 'identifier', 'label', 'source_field', 'normalization_state'], 'properties': {'label': {'type': 'string', 'title': 'Label'}, 'identifier': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Identifier'}, 'entity_type': {'enum': ['gene', 'variant', 'phenotype', 'pmid', 'doi', 'pmcid', 'omim'], 'type': 'string', 'title': 'Entity Type'}, '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'], 'type': 'string', 'title': 'Source Field'}, 'normalization_state': {'enum': ['normalized', 'source_indexed'], 'type': 'string', 'title': 'Normalization State'}}, 'additionalProperties': False}}, 'title': 'PublicCorpusSearchResponse', 'required': ['contract_version', 'query', 'returned_count', 'results', 'searchable_fields', 'usage_boundary'], 'properties': {'query': {'type': 'string', 'title': 'Query'}, 'results': {'type': 'array', 'items': {'$ref': '#/$defs/PublicCorpusSearchResult'}, 'title': 'Results'}, 'has_more': {'type': 'boolean', 'title': 'Has More', 'default': False}, 'graph_used': {'type': 'boolean', 'title': 'Graph Used', 'default': False}, 'next_cursor': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Next Cursor', 'default': None}, 'graph_version': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Graph Version', 'default': None}, 'returned_count': {'type': 'integer', 'title': 'Returned Count'}, 'usage_boundary': {'type': 'object', 'title': 'Usage Boundary', 'additionalProperties': True}, 'contract_version': {'type': 'string', 'const': '1.0', 'title': 'Contract Version'}, 'searchable_fields': {'type': 'array', 'items': {'type': 'string'}, 'title': 'Searchable Fields'}, 'semantic_index_used': {'type': 'boolean', 'title': 'Semantic Index Used', 'default': False}, 'graph_degraded_reason': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Graph Degraded Reason', 'default': None}, 'semantic_degraded_reason': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Semantic Degraded Reason', 'default': None}}, 'additionalProperties': False}
search_variant_evidence
Classify or interpret a germline variant under ACMG/AMP
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.
Read only Idempotent
Input schema 
{'type': 'object', 'title': 'SearchVariantArguments', 'required': ['query'], 'properties': {'query': {'type': 'string', 'title': 'Query', 'maxLength': 512, 'minLength': 1, '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.'}, 'assembly': {'type': 'string', 'const': 'GRCh38', 'title': 'Assembly', 'default': 'GRCh38', 'description': 'Reference genome assembly. Folklore currently accepts GRCh38 only.'}}, 'description': 'The only public scientific input admitted by the MCP tool.', 'additionalProperties': False}
Output schema 
{'type': 'object', 'required': ['contract_version', 'record_url', 'result', 'usage_boundary', 'adapter_error'], 'properties': {'result': {'anyOf': [{'type': 'object', 'required': ['search_contract_version', 'status'], 'properties': {'status': {'enum': ['resolved', 'ambiguous', 'not_found', 'invalid_request', 'unsupported', 'resolution_unavailable'], 'type': 'string'}, 'search_contract_version': {'type': 'string', 'const': '1.0'}}, 'additionalProperties': True}, {'type': 'null'}]}, 'record_url': {'type': ['string', 'null'], 'format': 'uri'}, 'adapter_error': {'anyOf': [{'type': 'object', 'required': ['code', 'message', 'retryable'], 'properties': {'code': {'type': 'string', 'minLength': 1}, 'message': {'type': 'string', 'minLength': 1}, 'retryable': {'type': 'boolean'}}, 'additionalProperties': False}, {'type': 'null'}]}, 'usage_boundary': {'type': 'object', 'required': ['result_type', 'review_required', 'patient_context_evaluated', 'intended_use', 'not_for'], 'properties': {'not_for': {'type': 'array', 'items': {'enum': ['patient_diagnosis', 'treatment_decision', 'standalone_clinical_reporting'], 'type': 'string'}, 'maxItems': 3, 'minItems': 3, 'uniqueItems': True}, 'result_type': {'type': 'string', 'const': 'automated_variant_level_classification'}, 'intended_use': {'type': 'string', 'const': 'professional_variant_review'}, 'review_required': {'type': 'boolean', 'const': True}, 'patient_context_evaluated': {'type': 'boolean', 'const': False}}, 'additionalProperties': False}, 'contract_version': {'type': 'string', 'const': '1'}}, 'additionalProperties': False}
search_variant_literature
Find literature for a germline variant
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 Idempotent
Input schema 
{'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': None, '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}
Output schema 
{'type': 'object', '$defs': {'CorpusProvenance': {'type': 'object', 'title': 'CorpusProvenance', 'required': ['source', 'publication_count', 'latest_publication_date', 'retrieved_at', 'semantic_index_used'], 'properties': {'source': {'type': 'string', 'const': 'Helena Literature Corpus canonical works', 'title': 'Source'}, 'retrieved_at': {'type': 'string', 'title': 'Retrieved At'}, 'publication_count': {'type': 'integer', 'title': 'Publication Count'}, 'semantic_index_used': {'type': 'boolean', 'title': 'Semantic Index Used'}, 'latest_publication_date': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Latest Publication Date'}}, 'additionalProperties': False}, 'LiteraturePublication': {'type': 'object', 'title': 'LiteraturePublication', 'required': ['pmid', 'title', 'abstract_excerpt', 'journal', 'publication_date', 'doi', 'pmc_id', 'pubmed_url', 'match_type', 'matched_variant', 'mention_context', 'phenotype_terms', 'structured_score'], 'properties': {'doi': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Doi'}, 'pmid': {'type': 'string', 'title': 'Pmid', 'pattern': '^[0-9]{1,12}$'}, 'title': {'type': 'string', 'title': 'Title'}, 'pmc_id': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Pmc Id'}, 'journal': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Journal'}, 'match_type': {'enum': ['exact_variant', 'variant_alias', 'gene_association'], 'type': 'string', 'title': 'Match Type'}, 'pubmed_url': {'type': 'string', 'title': 'Pubmed Url'}, 'matched_variant': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Matched Variant'}, 'mention_context': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Mention Context'}, 'phenotype_terms': {'type': 'array', 'items': {'type': 'string'}, 'title': 'Phenotype Terms'}, 'abstract_excerpt': {'type': 'string', 'title': 'Abstract Excerpt'}, 'publication_date': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Publication Date'}, 'structured_score': {'type': 'number', 'title': 'Structured Score'}}, 'additionalProperties': False}, 'LiteratureAuthorityResponse': {'type': 'object', 'title': 'LiteratureAuthorityResponse', 'required': ['contract_version', 'assembly', 'canonical_key', 'gene_symbol', 'aliases', 'question', 'candidate_count', 'publications', 'provenance', 'limitations'], 'properties': {'aliases': {'type': 'array', 'items': {'type': 'string'}, 'title': 'Aliases'}, 'assembly': {'type': 'string', 'const': 'GRCh38', 'title': 'Assembly'}, 'question': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'title': 'Question'}, 'provenance': {'$ref': '#/$defs/CorpusProvenance'}, 'gene_symbol': {'type': 'string', 'title': 'Gene Symbol'}, 'limitations': {'type': 'array', 'items': {'type': 'string'}, 'title': 'Limitations'}, 'publications': {'type': 'array', 'items': {'$ref': '#/$defs/LiteraturePublication'}, 'title': 'Publications'}, 'canonical_key': {'type': 'string', 'title': 'Canonical Key'}, 'candidate_count': {'type': 'integer', 'title': 'Candidate Count'}, 'contract_version': {'type': 'string', 'const': '1.0', 'title': 'Contract Version'}}, 'additionalProperties': False}}, 'title': 'PublicVariantLiteratureResponse', 'required': ['status', 'variant_result', 'literature', 'usage_boundary'], 'properties': {'status': {'enum': ['resolved', 'ambiguous', 'not_found', 'invalid_request', 'unsupported', 'resolution_unavailable'], 'type': 'string', 'title': 'Status'}, 'literature': {'anyOf': [{'$ref': '#/$defs/LiteratureAuthorityResponse'}, {'type': 'null'}]}, 'usage_boundary': {'type': 'object', 'title': 'Usage Boundary', 'additionalProperties': True}, 'variant_result': {'type': 'object', 'title': 'Variant Result', 'additionalProperties': True}, 'contract_version': {'type': 'string', 'const': '1.0', 'title': 'Contract Version', 'default': '1.0'}}, 'additionalProperties': False}
support_helena
Support Helena's free scientific infrastructure
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 Idempotent
Input schema 
{'type': 'object', 'properties': {}, 'additionalProperties': False}
Output schema 
{'type': 'object', 'additionalProperties': True}
History

Recent tool changes

Added
search_disease_genes
Sept. 17, 2026, 12:42 p.m.
Added
get_gene_disease_associations
Sept. 17, 2026, 12:42 p.m.
Added
support_helena
Sept. 17, 2026, 12:42 p.m.
Added
search_literature_corpus
Sept. 17, 2026, 12:42 p.m.
Added
get_publication_details
Sept. 17, 2026, 12:42 p.m.
Added
search_variant_literature
Sept. 17, 2026, 12:42 p.m.
Added
search_variant_evidence
Sept. 17, 2026, 12:42 p.m.
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