HTTP GET with rate-limiting, caching, and 429 retry.

Get item from cache if not expired.

Run command with own globals/locals and returns anything printed. Timeout after the specified number of seconds.

Parse a unified search query.

Search PubMed and return PMIDs. Args: query: Search query max_results: Maximum number of results

Update the internal Gaussian Process with new data.

Run a test function with timing and error handling.

Get cached response if available and not expired.

Search bioRxiv or medRxiv for articles. Note: Due to API limitations, this performs client-side filtering on recent articles only. Se

Run a single test and track results.

Parse a VCF file (supports .vcf, .vcf.gz). Args: vcf_path: Path to VCF file max_variants: Maximum variants to parse (0 = unl

Load ToolUniverse instance.

Save all modified XML files to disk and copy to destination directory. This persists all changes made via add_comment() and reply_to

* Format detection result for display

General helper function to query REST APIs with consistent error handling. Parameters ---------- endpoint (str): Full URL endpoint to que

Register an endpoint for tracking. Args: key: Unique identifier for the endpoint endpoint: Endpoint metadata includin

Write a Newick tree string to a file.

Helper function to query LLMs for generating API calls based on natural language prompts. Supports multiple model providers including Claude, Gem

Write a FASTA alignment file from a dict of {name: sequence}.

Convert a TrialQuery object into a dict of query params for the ClinicalTrials.gov API (v2). Each key maps to one or more strings in a list, c

Convert a value to a list if it's not already. This is particularly useful for handling inputs from LLMs that might provide comma-separa

Fetch comprehensive details for a specific biomedical record. This tool retrieves full information for articles, clinical trials, genetic variant

Return False to suppress the log record, True to allow it.

HTTP POST with rate-limiting, caching, and 429 retry.

Calculate percentile.

A general-purpose formatter for query function results to reduce output size. Parameters ---------- result (dict): The original API respo

Create a temporary directory with fungi and animal subdirectories, each containing several alignment (.fa) and tree (.nwk) files.

Log message if verbose mode is enabled.

Log message if verbose mode is enabled.

Generic query method for any FDA endpoint. Args: category: API category (drug, device, food, animalandveterinary, other)

Search biomedical literature, clinical trials, genetic variants, genes, drugs, and diseases. ⚠️ IMPORTANT: Have you used the 'think' tool first?

Search FDA drug recall records from Enforcement database. Args: drug: Drug name (brand or generic) to search for recall_clas

Execute function through circuit breaker. Args: func: Async function to execute *args: Positional arguments for func

Evaluate a test result and record it. eval_mode: - 'range': expected is (low, high), value must be within - 'exact': expected is exac

Predict variant effects using AlphaGenome. Args: chromosome: Chromosome (e.g., 'chr7') position: 1-based genomic position

Map VCF consequence annotation to standardized mutation type.

Build profiles from demo patient for reuse across tests.

Check if a protein change matches the filter criteria. Args: protein_change: The protein change to check Returns:

Safely extract text from XML element

Log message if verbose mode is enabled.

Format search results according to OpenAI MCP search semantics. Converts domain-specific result formats into a standardized structure with: -

Make a POST request to cBioPortal API. Args: path: API path data: Request body data endpoint_key: Registr

Convert config to dictionary for easy access.

Clean and normalize text from FDA data.

Format a single gene result. Args: result: Raw gene data from MyGene.info API Returns: Standardized gene res

Get details of a clinical trial by module.

Search FDA drug shortage records. Args: drug: Drug name (generic or brand) to search for status: Shortage status (current, r

Search for articles across PubMed and preprint sources.

Extract gene and AA change in format like 'BRAF V600A' from variant data.

Clear metrics. Args: name: Specific metric to clear, or None to clear all

Get list of all curated genes in OncoKB. Returns genes that have been curated with oncogenic mutations and/or therapeutic implication

Prioritize causal variants at a genomic locus using GWAS fine-mapping. This function integrates statistical fine-mapping results from Open T

Search FDA drug approval records from Drugs@FDA. Args: drug: Drug name (brand or generic) to search for application_number:

Make API request with retry logic. Args: endpoint: API endpoint (e.g., '/works', '/authors') params: Query p

Filter variants based on criteria. Returns (passing, failing). Args: variants: List of VariantRecord criteria: FilterCriteri

Generate synthetic methylation beta-value matrix.

Get or create a connection pool for the current event loop.

Parse a BRENDA Km value entry into structured data.

Enforce NCBI rate limit of 3 requests/second.