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{ "count": 1108, "next": "?page=2", "previous": null, "list": [ { "name": "Folklore", "description": "Deterministic, rule-based variant interpretation platform for clinical genetics laboratories. Automates ACMG/AMP 2015 classification using a Bayesian point-based framework (Tavtigian et al. 2018) with BayesDel ClinGen SVI-calibrated thresholds (Pejaver et al. 2022). Integrates 8 reference databases (gnomAD v4.1, ClinVar, dbNSFP 4.9c, SpliceAI, gnomAD Constraint, HPO, ClinGen, Ensembl VEP). Analyzes nuclear and mtDNA variants, structural and copy-number variants (SV/CNV), with trio/family and cohort analysis. Supports HPO-based phenotype matching, biomedical literature mining across 2M+ PubMed publications, and structured clinical report generation. AI assists in evidence synthesis but does not make classification decisions. EU-hosted on dedicated infrastructure in Helsinki, Finland (GDPR-compliant).", "homepage": "https://folklore.helena.bio", "biotoolsID": "HelixInsight", "biotoolsCURIE": "biotools:HelixInsight", "version": [ "3.39.1" ], "otherID": [ { "value": "RRID:SCR_028669", "type": "rrid", "version": "3.39.1" } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3225", "term": "Variant classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2955", "term": "Sequence report" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0920", "term": "Genotype/phenotype report" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1622", "term": "Disease report" }, "format": [] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0305", "term": "Literature search" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web API", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3574", "term": "Human genetics" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "Proprietary", "collectionID": [], "maturity": "Mature", "cost": "Commercial", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/helena-bioinformatics/folklore-mcp", "type": [ "Repository" ], "note": "Public Apache-2.0 MCP protocol adapter source; the Folklore SaaS platform and clinical interpretation backend remain proprietary." }, { "url": "https://api.helena.bio/folklore/v1/mcp", "type": [ "Service" ], "note": "Public remote endpoint for Folklore Clinical Variant Interpretation MCP version 1.2.2." }, { "url": "https://registry.modelcontextprotocol.io/v0.1/servers?search=io.github.helena-bioinformatics%2Ffolklore&version=latest", "type": [ "Software catalogue" ], "note": "Official MCP Registry entry: io.github.helena-bioinformatics/folklore." }, { "url": "https://folklore.helena.bio/integrations", "type": [ "Other" ], "note": "Official Folklore integrations and MCP client connection page." }, { "url": "https://api.helena.bio/folklore/v1/health", "type": [ "Technical monitoring" ], "note": "Public health and discovery metadata endpoint for the Folklore MCP service." } ], "download": [ { "url": "https://github.com/helena-bioinformatics/folklore-mcp", "type": "Source code", "note": "Apache-2.0 standalone MCP protocol adapter. Excludes proprietary clinical interpretation logic, private data, credentials and operational infrastructure.", "version": "1.2.2" } ], "documentation": [ { "url": "https://folklore.helena.bio/docs", "type": [ "General" ], "note": "Complete production documentation covering every threshold, database version, and classification rule. Intended for clinical geneticists, laboratory directors, accreditation auditors, and bioinformaticians." }, { "url": "https://folklore.helena.bio/how-it-works", "type": [ "General" ], "note": "Seven-stage analysis pipeline (quality control, annotation, classification, phenotype matching, literature, screening, interpretation) transforming a raw VCF into a clinician-ready report, each stage producing traceable, auditable output." }, { "url": "https://folklore.helena.bio/methodology", "type": [ "General" ], "note": "ACMG/AMP 2015 classification methodology (Richards et al. 2015) via Bayesian point-based system (Tavtigian et al. 2018), BayesDel ClinGen SVI-calibrated thresholds (Pejaver et al. 2022), and SpliceAI aligned to ClinGen SVI 2023 (Walker et al. 2023). Optional ClinGen VCEP overlay for ~50-60 genes. Strictly evidence-based, no ML determines pathogenicity." }, { "url": "https://folklore.helena.bio/methodology/mtdna", "type": [ "General" ], "note": "Mitochondrial DNA variant classification under the ClinGen Mitochondrial Disease Working Group (MMDWG) 2020 specification (McCormick et al. 2020). Operates as an independent module from the nuclear ACMG/AMP pipeline; every variant carries an explicit framework provenance label. Strength tiers follow ClinGen mtDNA VCEP v1.0.0." }, { "url": "https://folklore.helena.bio/methodology/family-analysis", "type": [ "General" ], "note": "Inheritance-aware evidence from trio (proband + both parents), duo, and proband-plus-sibling analyses. Implements ClinGen SVI 2018 de novo PS2/PM6 (PMID 29543229), Jarvik & Browning 2016 LOD segregation framework (PMID 27236918), and ClinGen SVI 2021 PP1 strength bands. Augments the existing ACMG/AMP classification without re-calling variants." }, { "url": "https://folklore.helena.bio/methodology/sv", "type": [ "General" ], "note": "Structural and copy-number variant evaluation under the Riggs 2020 joint ACMG/ClinGen technical standard. Documents the point-based loss and gain metrics, dosage-sensitivity evidence, and five-tier classification, with reference data and documented limitations." }, { "url": "https://folklore.helena.bio/screening-methodology", "type": [ "General" ], "note": "Prioritizes classified variants for clinical review. After ACMG classification determines what each variant is, screening determines which to review first based on patient-specific clinical relevance. Evaluates seven independent dimensions, applies clinical profile boosts, and produces a four-tier priority ranking with transparent, visible score components." }, { "url": "https://folklore.helena.bio/docs/folklore-connector", "type": [ "API documentation" ], "note": "Canonical connector guide for Folklore Clinical Variant Interpretation MCP (io.github.helena-bioinformatics/folklore), version 1.2.2." }, { "url": "https://github.com/helena-bioinformatics/folklore-mcp#readme", "type": [ "General" ], "note": "Public Apache-2.0 MCP protocol adapter README. The Folklore SaaS platform and clinical interpretation backend remain proprietary." }, { "url": "https://github.com/helena-bioinformatics/folklore-mcp/blob/main/CHANGELOG.md", "type": [ "Release notes" ], "note": "Release history for the public Folklore MCP protocol adapter." } ], "publication": [ { "doi": "10.5281/zenodo.21105027", "pmid": null, "pmcid": null, "type": [ "Preprint" ], "version": "1.0", "note": "Methodological framework for real-world performance studies of the platform's variant classification, demonstrated on three internal validation cohorts.", "metadata": null }, { "doi": "10.5281/zenodo.21189571", "pmid": null, "pmcid": null, "type": [ "Preprint" ], "version": "1.0", "note": "A Deterministic Classification Core with an Agentic Interpretation Layer: An Architecture for Auditable, Human-Gated Clinical Variant Analysis", "metadata": null }, { "doi": "10.5281/zenodo.21763096", "pmid": null, "pmcid": null, "type": [ "Preprint" ], "version": null, "note": "Robustness and cross-cohort concordance of developmental regulons in endometrial carcinoma. Authors: Draga Toncheva, Vasil Sgurev and Vladimir Mitev.", "metadata": null }, { "doi": "10.5281/zenodo.21922952", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": "1.2.2", "note": "Archived public Apache-2.0 Folklore MCP adapter release. 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Serves one record per gene combining Pfam domains, ESMFold structures with Foldseek search, protein language-model features, orthology, curated knowledge, protein association networks and intra-species selection inferred from 145209 sequenced genomes, with dated sources and a graded confidence level for every field. Intended as a successor to Mycobrowser, which is no longer maintained.", "homepage": "https://mtbc.gclab.fr", "biotoolsID": "mtbc_gene_atlas", "biotoolsCURIE": "biotools:mtbc_gene_atlas", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" }, { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1026", "term": "Gene symbol" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2295", "term": "Gene ID" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0916", "term": "Gene report" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1277", "term": "Protein features" }, "format": [] } ], "note": "Query by H37Rv locus tag (Rv1908c) or gene name (katG); every field carries its provenance and confidence.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0331", "term": "Variant effect prediction" }, { "uri": "http://edamontology.org/operation_0303", "term": "Protein fold recognition" } ], "input": [], "output": [], "note": "Structure-based leads for genes with no domain assignment, and population-scale selection signal per gene.", "cmd": null } ], "toolType": [ "Web application", "Database portal", "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_0085", "term": "Functional genomics" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3301", "term": "Microbiology" }, { "uri": "http://edamontology.org/topic_0736", "term": "Protein folds and structural domains" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "CC-BY-4.0", "collectionID": [ "Mycobacterium tuberculosis complex" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/cguyeux/mtbc-gene-atlas", "type": [ "Repository" ], "note": "Source code repository, one script per evidence layer (MIT license)." } ], "download": [ { "url": "https://doi.org/10.5281/zenodo.20815246", "type": "Downloads page", "note": "Zenodo concept DOI: resolves to the latest archived release (per-gene records, consolidated layers, reproducibility bundle).", "version": null }, { "url": "https://mtbc.gclab.fr/api/v1", "type": "API specification", "note": "Versioned read-only REST API over the served records.", "version": null } ], "documentation": [ { "url": "https://mtbc.gclab.fr/about", "type": [ "General" ], "note": "Scope, evidence layers, citation and coordinate-system conventions." } ], "publication": [ { "doi": "10.5281/zenodo.20815246", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": "Archived data and code releases (concept DOI). 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