description = [
    {
        "description": "Query the UniProt REST API using either natural language or a direct endpoint.",
        "name": "query_uniprot",
        "optional_parameters": [
            {
                "default": None,
                "description": "Full or partial UniProt API endpoint URL to query directly (e.g., 'https://rest.uniprot.org/uniprotkb/P01308')",
                "name": "endpoint",
                "type": "str",
            },
            {"default": 5, "description": "Maximum number of results to return", "name": "max_results", "type": "int"},
        ],
        "required_parameters": [
            {
                "default": None,
                "description": 'Natural language query about proteins (e.g., "Find information about human insulin")',
                "name": "prompt",
                "type": "str",
            }
        ],
    },
    {
        "description": "Query the AlphaFold Database API for protein structure predictions or metadata; optionally download structures.",
        "name": "query_alphafold",
        "optional_parameters": [
            {
                "name": "endpoint",
                "type": "str",
                "description": "Endpoint: 'prediction', 'summary', or 'annotations'",
                "default": "prediction",
            },
            {"name": "residue_range", "type": "str", "description": "Residue range as 'start-end'", "default": None},
            {"name": "download", "type": "bool", "description": "Whether to download structure file", "default": False},
            {"name": "output_dir", "type": "str", "description": "Directory to save downloaded files", "default": None},
            {"name": "file_format", "type": "str", "description": "Download format 'pdb' or 'cif'", "default": "pdb"},
            {
                "name": "model_version",
                "type": "str",
                "description": "AlphaFold model version (e.g., v4)",
                "default": "v4",
            },
            {"name": "model_number", "type": "int", "description": "Model number (1-5)", "default": 1},
        ],
        "required_parameters": [
            {
                "name": "uniprot_id",
                "type": "str",
                "description": "UniProt accession ID (e.g., 'P12345')",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the InterPro REST API using natural language or a direct endpoint.",
        "name": "query_interpro",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "Endpoint path or full URL", "default": None},
            {"name": "max_results", "type": "int", "description": "Max results per page", "default": 3},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about protein domains/families",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the RCSB PDB database using natural language or a direct structured query.",
        "name": "query_pdb",
        "optional_parameters": [
            {"name": "query", "type": "dict", "description": "Direct RCSB Search API query JSON", "default": None},
            {"name": "max_results", "type": "int", "description": "Maximum results to return", "default": 3},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about protein structures",
                "default": None,
            }
        ],
    },
    {
        "description": "Retrieve detailed data and/or download files for PDB identifiers.",
        "name": "query_pdb_identifiers",
        "optional_parameters": [
            {
                "name": "return_type",
                "type": "str",
                "description": "'entry', 'assembly', 'polymer_entity', etc.",
                "default": "entry",
            },
            {"name": "download", "type": "bool", "description": "Download PDB structure files", "default": False},
            {
                "name": "attributes",
                "type": "List[str]",
                "description": "Specific attributes to retrieve",
                "default": None,
            },
        ],
        "required_parameters": [
            {"name": "identifiers", "type": "List[str]", "description": "List of PDB identifiers", "default": None}
        ],
    },
    {
        "description": "Take a natural language prompt and convert it to a structured KEGG API query.",
        "name": "query_kegg",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "Direct KEGG endpoint to query", "default": None},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {"name": "prompt", "type": "str", "description": "Natural language query about KEGG data", "default": None}
        ],
    },
    {
        "description": "Query the STRING protein interaction database using natural language or direct endpoint.",
        "name": "query_stringdb",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "Full URL to query directly", "default": None},
            {
                "name": "download_image",
                "type": "bool",
                "description": "Download image results if endpoint is image",
                "default": False,
            },
            {"name": "output_dir", "type": "str", "description": "Directory to save downloaded files", "default": None},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about protein interactions",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the IUCN Red List API using natural language or a direct endpoint.",
        "name": "query_iucn",
        "optional_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about species conservation status",
                "default": None,
            },
            {"name": "endpoint", "type": "str", "description": "Endpoint name or full URL", "default": None},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [{"name": "token", "type": "str", "description": "IUCN API token", "default": ""}],
    },
    {
        "description": "Query the Paleobiology Database (PBDB) API using natural language or a direct endpoint.",
        "name": "query_paleobiology",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "API endpoint name or full URL", "default": None},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about fossil records",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the JASPAR REST API for transcription factor binding profiles.",
        "name": "query_jaspar",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "API endpoint path or full URL", "default": None},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about TF binding profiles",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the World Register of Marine Species (WoRMS) REST API using natural language or a direct endpoint.",
        "name": "query_worms",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "Full URL or endpoint specification", "default": None},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about marine species",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the cBioPortal REST API using natural language or a direct endpoint.",
        "name": "query_cbioportal",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "API endpoint path or full URL", "default": None},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about cancer genomics",
                "default": None,
            }
        ],
    },
    {
        "description": "Convert a natural language prompt into a structured ClinVar search query and run it.",
        "name": "query_clinvar",
        "optional_parameters": [
            {"name": "search_term", "type": "str", "description": "Direct ClinVar search term", "default": None},
            {"name": "max_results", "type": "int", "description": "Maximum number of results", "default": 3},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about genetic variants",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the NCBI GEO database (GDS/GEOPROFILES) using natural language or direct search term.",
        "name": "query_geo",
        "optional_parameters": [
            {"name": "search_term", "type": "str", "description": "Direct GEO search term", "default": None},
            {"name": "max_results", "type": "int", "description": "Maximum number of results", "default": 3},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about expression data",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the NCBI dbSNP database using natural language or direct search term.",
        "name": "query_dbsnp",
        "optional_parameters": [
            {"name": "search_term", "type": "str", "description": "Direct dbSNP search term", "default": None},
            {"name": "max_results", "type": "int", "description": "Maximum number of results", "default": 3},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about SNPs/variants",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the UCSC Genome Browser API using natural language or a direct endpoint.",
        "name": "query_ucsc",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "Full URL or endpoint spec", "default": None},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about genomic data",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the Ensembl REST API using natural language or a direct endpoint.",
        "name": "query_ensembl",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "Direct Ensembl endpoint or full URL", "default": None},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about genomic data",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the OpenTargets Platform API using natural language or a direct GraphQL query.",
        "name": "query_opentarget",
        "optional_parameters": [
            {"name": "query", "type": "str", "description": "Direct GraphQL query string", "default": None},
            {"name": "variables", "type": "dict", "description": "Variables for GraphQL", "default": None},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": False},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about targets/diseases",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the Monarch Initiative API using natural language or a direct endpoint.",
        "name": "query_monarch",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "Direct endpoint or full URL", "default": None},
            {"name": "max_results", "type": "int", "description": "Max results (adds limit param)", "default": 2},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": False},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about genes/diseases/phenotypes",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the OpenFDA API using natural language or direct parameters.",
        "name": "query_openfda",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "Direct endpoint or full URL", "default": None},
            {"name": "max_results", "type": "int", "description": "Max results (limit)", "default": 100},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
            {"name": "search_params", "type": "dict", "description": "Search parameters mapping", "default": None},
            {"name": "sort_params", "type": "dict", "description": "Sort parameters mapping", "default": None},
            {"name": "count_params", "type": "str", "description": "Field to count", "default": None},
            {"name": "skip_results", "type": "int", "description": "Skip for pagination", "default": 0},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about OpenFDA data",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the GWAS Catalog API using natural language or a direct endpoint.",
        "name": "query_gwas_catalog",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "Endpoint name (e.g., 'studies')", "default": None},
            {"name": "max_results", "type": "int", "description": "Max results per page (size)", "default": 3},
        ],
        "required_parameters": [
            {"name": "prompt", "type": "str", "description": "Natural language query about GWAS data", "default": None}
        ],
    },
    {
        "description": "Query gnomAD for variants in a gene using natural language or direct gene symbol.",
        "name": "query_gnomad",
        "optional_parameters": [
            {"name": "gene_symbol", "type": "str", "description": "Gene symbol (e.g., 'BRCA1')", "default": None},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about genetic variants",
                "default": None,
            }
        ],
    },
    {
        "description": "Identify a DNA or protein sequence using NCBI BLAST.",
        "name": "blast_sequence",
        "optional_parameters": [],
        "required_parameters": [
            {"name": "sequence", "type": "str", "description": "Query sequence", "default": None},
            {"name": "database", "type": "str", "description": "BLAST database (e.g., core_nt or nr)", "default": None},
            {"name": "program", "type": "str", "description": "BLAST program (blastn or blastp)", "default": None},
        ],
    },
    {
        "description": "Query the Reactome database using natural language or a direct endpoint; optionally download pathway diagrams.",
        "name": "query_reactome",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "Direct endpoint or full URL", "default": None},
            {
                "name": "download",
                "type": "bool",
                "description": "Download pathway diagram if available",
                "default": False,
            },
            {"name": "output_dir", "type": "str", "description": "Directory to save downloads", "default": None},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about biological pathways",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the RegulomeDB database using natural language or direct endpoint.",
        "name": "query_regulomedb",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "Direct RegulomeDB endpoint URL", "default": None},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": False},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about regulatory elements",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the PRIDE proteomics database using natural language or a direct endpoint.",
        "name": "query_pride",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "Full endpoint to query", "default": None},
            {"name": "max_results", "type": "int", "description": "Maximum number of results", "default": 3},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about proteomics data",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the Guide to PHARMACOLOGY (GtoPdb) database using natural language or a direct endpoint.",
        "name": "query_gtopdb",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "Full API endpoint to query", "default": None},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about drug targets/ligands/interactions",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the ReMap database for regulatory elements and transcription factor binding.",
        "name": "query_remap",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "Full API endpoint to query", "default": None},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about TF binding sites",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the Mouse Phenome Database (MPD) using natural language or a direct endpoint.",
        "name": "query_mpd",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "Full API endpoint to query", "default": None},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about mouse phenotypes/strains",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the Electron Microscopy Data Bank (EMDB) using natural language or a direct endpoint.",
        "name": "query_emdb",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "Full API endpoint to query", "default": None},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about EM structures",
                "default": None,
            }
        ],
    },
    {
        "description": "Query Synapse REST API for biomedical datasets/files using natural language or structured search parameters. Supports optional authentication via SYNAPSE_AUTH_TOKEN.",
        "name": "query_synapse",
        "optional_parameters": [
            {
                "name": "query_term",
                "type": "str|list[str]",
                "description": "Search term(s) (AND logic across list)",
                "default": None,
            },
            {
                "name": "return_fields",
                "type": "list[str]",
                "description": "Fields to return",
                "default": ["name", "node_type", "description"],
            },
            {"name": "max_results", "type": "int", "description": "Max results (20 typical, up to 50)", "default": 20},
            {
                "name": "query_type",
                "type": "str",
                "description": "'dataset', 'file', or 'folder'",
                "default": "dataset",
            },
            {
                "name": "verbose",
                "type": "bool",
                "description": "Return full API response or formatted",
                "default": True,
            },
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about biomedical data",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the PubChem PUG-REST API using natural language or a direct endpoint.",
        "name": "query_pubchem",
        "optional_parameters": [
            {
                "name": "endpoint",
                "type": "str",
                "description": "Direct PubChem API endpoint or full URL",
                "default": None,
            },
            {"name": "max_results", "type": "int", "description": "Max results (rate-limited to 5 rps)", "default": 5},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about chemical compounds",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the ChEMBL REST API via natural language, direct endpoint, or identifiers (chembl_id, smiles, molecule_name).",
        "name": "query_chembl",
        "optional_parameters": [
            {
                "name": "endpoint",
                "type": "str",
                "description": "Direct ChEMBL API endpoint or full URL",
                "default": None,
            },
            {"name": "chembl_id", "type": "str", "description": "ChEMBL ID (e.g., 'CHEMBL25')", "default": None},
            {"name": "smiles", "type": "str", "description": "SMILES for similarity/substructure", "default": None},
            {"name": "molecule_name", "type": "str", "description": "Molecule name to search", "default": None},
            {"name": "max_results", "type": "int", "description": "Max results", "default": 20},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about bioactivity data",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the UniChem 2.0 REST API using natural language or a direct endpoint.",
        "name": "query_unichem",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "Direct UniChem endpoint or full URL", "default": None},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about chemical cross-references",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the ClinicalTrials.gov API v2 using natural language or a direct endpoint.",
        "name": "query_clinicaltrials",
        "optional_parameters": [
            {
                "name": "endpoint",
                "type": "str",
                "description": "Direct ClinicalTrials.gov endpoint or full URL",
                "default": None,
            },
            {"name": "max_results", "type": "int", "description": "Page size for results (pageSize)", "default": 10},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about clinical trials",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the DailyMed RESTful API using natural language or a direct endpoint.",
        "name": "query_dailymed",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "Direct DailyMed endpoint or full URL", "default": None},
            {"name": "format", "type": "str", "description": "'json' or 'xml'", "default": "json"},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about drug labeling",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the QuickGO API using natural language or a direct endpoint.",
        "name": "query_quickgo",
        "optional_parameters": [
            {"name": "endpoint", "type": "str", "description": "Direct QuickGO endpoint or full URL", "default": None},
            {"name": "max_results", "type": "int", "description": "Max results (limit, up to 100)", "default": 25},
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about GO terms/annotations",
                "default": None,
            }
        ],
    },
    {
        "description": "Query the ENCODE Portal API to locate functional genomics data (experiments, files, biosamples, datasets).",
        "name": "query_encode",
        "optional_parameters": [
            {
                "name": "endpoint",
                "type": "str",
                "description": "Direct ENCODE Portal endpoint or full URL",
                "default": None,
            },
            {
                "name": "max_results",
                "type": "int|str",
                "description": "Limit for search endpoints (number or 'all')",
                "default": 25,
            },
            {"name": "verbose", "type": "bool", "description": "Return detailed results", "default": True},
        ],
        "required_parameters": [
            {
                "name": "prompt",
                "type": "str",
                "description": "Natural language query about functional genomics data",
                "default": None,
            }
        ],
    },
    {
        "description": "Given genomic coordinates, retrieve intersecting ENCODE SCREEN cCREs.",
        "name": "region_to_ccre_screen",
        "optional_parameters": [
            {"name": "assembly", "type": "str", "description": "Genome assembly (e.g., 'GRCh38')", "default": "GRCh38"}
        ],
        "required_parameters": [
            {"name": "coord_chrom", "type": "str", "description": "Chromosome (e.g., 'chr12')", "default": None},
            {"name": "coord_start", "type": "int", "description": "Start coordinate", "default": None},
            {"name": "coord_end", "type": "int", "description": "End coordinate", "default": None},
        ],
    },
    {
        "description": "Given a cCRE accession, return k nearest genes sorted by distance.",
        "name": "get_genes_near_ccre",
        "optional_parameters": [
            {"name": "k", "type": "int", "description": "Number of nearby genes to return", "default": 10}
        ],
        "required_parameters": [
            {
                "name": "accession",
                "type": "str",
                "description": "ENCODE cCRE accession ID (e.g., 'EH38E1516980')",
                "default": None,
            },
            {"name": "assembly", "type": "str", "description": "Genome assembly (e.g., 'GRCh38')", "default": None},
            {
                "name": "chromosome",
                "type": "str",
                "description": "Chromosome of the cCRE (e.g., 'chr12')",
                "default": None,
            },
        ],
    },
]