folklore-clinical-variant-interpretation-mcp

Folklore Clinical Variant Interpretation MCP skill

Helena Bioinformatics publishes Folklore Clinical Variant Interpretation MCP. Use its structured classification, reported criteria, source evidence and publication records.

Operating rules

• For variant tools, accept only a public variant identifier or notation supported by the published GRCh38 germline nuclear SNV and simple-indel contract.
• Call get_gene_disease_associations for one exact gene symbol/HGNC identifier; call search_disease_genes for an exact MONDO identifier or disease-name substring. Preserve distinct disease identities, source assertions, inheritance, evidence assessments and dates. These tools return ClinGen Gene-Disease Validity assertions. Empty results describe the queried snapshot.
• Call classify_germline_variant to classify and assess one supported variant.
• Read JSON-RPC errors first, then adapter_error when structuredContent.result is null.
• For variant interpretation, branch on structuredContent.result.status: resolved, ambiguous, not_found, invalid_request, unsupported or resolution_unavailable. A resolved identity with interpretation.status unavailable does not provide a classification.
• Ambiguous candidates are never selected automatically. Report the candidates and stop for user selection.
• Treat invalid_request, unsupported, not_found and resolution_unavailable as distinct outcomes. Do not replace any of them with a guess from model memory.
• Use search_variant_literature only with one supported public variant query. Literature matches retain their source labels alongside the variant classification.
• Use get_publication_details for a PMID returned by the literature tools and preserve the returned PMID, DOI, PMCID and source links.
• Use search_literature_corpus for a bounded scientific literature question or an exact publication identifier. Preserve provenance and match reasons.

For general publication discovery or citation and semantic graph exploration, prefer Noodle when available. Resolve exact variant identity with Folklore first for combined tasks. A general VUS explanation needs no variant lookup.