{
  "$schema": "https://modelcontextprotocol.io/schemas/mcp-server-card.json",
  "name": "fanta.bio",
  "description": "Functional genome annotations for studying gene regulation — query CREs (cis-regulatory elements), genes, SNPs, expression data, and ChIP-Atlas transcription factor binding directly from AI assistants.",
  "version": "1.0.0",
  "endpoint": "https://mcp.fanta.bio/mcp",
  "transport": "streamable-http",
  "protocolVersion": "2025-03-26",
  "publisher": {
    "name": "fanta.bio",
    "url": "https://fanta.bio"
  },
  "documentation": "https://docs.fanta.bio/mcp/",
  "license": "CC-BY-4.0",
  "categories": ["bioinformatics", "genomics", "research", "scientific-data"],
  "capabilities": {
    "tools": true,
    "prompts": true,
    "resources": true
  },
  "tools": [
    {"name": "search_genes", "description": "Search genes by ID, symbol, name, or synonym"},
    {"name": "search_snps", "description": "Search SNPs by rs ID or GWAS trait"},
    {"name": "search_cres", "description": "Filter CREs by ID, name, antigen, or external ID with wildcard support"},
    {"name": "search_cres_fulltext", "description": "Full-text keyword search across CREs"},
    {"name": "find_cres_by_region", "description": "Find CREs within a chromosome coordinate range"},
    {"name": "get_gene_details", "description": "Full gene record by Ensembl ID, symbol, or synonym"},
    {"name": "get_snp_details", "description": "Full SNP record by rs ID"},
    {"name": "get_cre_details", "description": "Full CRE annotation"},
    {"name": "find_cres_by_gene", "description": "All CREs associated with a gene, sorted by distance from TSS"},
    {"name": "find_cres_by_snp", "description": "All CREs near a SNP, sorted by distance"},
    {"name": "get_unique_antigens", "description": "Unique TFs binding any of a list of CREs"},
    {"name": "get_cres_batch", "description": "Batch lookup of full CRE annotations by ID"},
    {"name": "get_cre_expression", "description": "Expression vector for one CRE across all samples"},
    {"name": "get_gene_expression", "description": "Expression for the CREs associated with a gene"},
    {"name": "get_cre_bound_tfs", "description": "ChIP-Atlas TF binding for one CRE with Q-scores"},
    {"name": "get_gene_antigens", "description": "Unique TFs binding any of a gene's associated CREs"},
    {"name": "find_shared_regulators", "description": "TFs shared across a set of CREs or genes"},
    {"name": "get_gene_regulatory_summary", "description": "Gene info + associated CREs + top regulating TFs"},
    {"name": "get_snp_regulatory_impact", "description": "SNP info + affected CREs + bound TFs"}
  ],
  "prompts": [
    {"name": "find_gene_tfs", "description": "Surface all TFs that regulate a gene, ranked by binding evidence"},
    {"name": "compare_genes_regulation", "description": "Compare two genes' regulatory landscapes; highlight shared TFs"},
    {"name": "region_regulatory_analysis", "description": "Analyze every CRE in a genomic region and the TFs active there"},
    {"name": "disease_snp_analysis", "description": "Find disease-associated SNPs and analyze their regulatory impact"},
    {"name": "explore_cre_expression", "description": "Explore one CRE's expression pattern, binding TFs, and nearest gene"}
  ],
  "resources": [
    {"uri": "organisms://list", "description": "Supported organisms with assembly aliases"},
    {"uri": "schema://database", "description": "Detailed table-by-table description of the underlying D1 schema"}
  ]
}