| 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, |
| }, |
| ], |
| }, |
| ] |
|
|
