Get summary statistics for a metric. Args: name: Metric name Returns: Summary statistics or None if metric not found

Fetch variant data from TCGA/GDC. Args: variant_id: Can be gene AA change (e.g., "BRAF V600E") or genomic coordinates

Search ClinicalTrials.gov for clinical trials.

Append a line to 'lines', avoiding consecutive blank lines. :param lines: The running list of lines to which we add. :param line: The line to

Simulate tool calls with realistic responses.

Convert energy between units.

Convert force between units.

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

Get user-friendly instructions for obtaining and setting the API key. Returns: Formatted string with instructions

Get helpful suggestions for invalid channels.

Get the appropriate handler class for a domain. Args: domain: The domain name ('article', 'trial', 'variant', 'gene', 'drug', 'disease',

Get detailed drug approval information for a specific application. Args: application_number: NDA or BLA application number

Get detailed drug recall information for a specific recall. Args: recall_number: FDA recall number api_key: Optional OpenFD

Check if an HTTP status code should trigger a retry. Args: status_code: HTTP status code config: Retry configuration Returns

List available NixOS channels with their status. Returns: Plain text list showing channel names, versions, and availability

Convert various input formats to lists. Handles: - JSON arrays: '["item1", "item2"]' -> ['item1', 'item2'] - Comma-separated:

Test a prompt with Anthropic API and verify expected behaviors.

Run a single evaluation scenario.

Safely get a value from a dictionary

Truncate text to a maximum length with ellipsis.

Validate API key format. Args: api_key: API key string Returns: Validated API key or None

GameAnalyticsApp örneğini tembel yükler (lazily initializes) ve döndürür. Bu fonksiyon, bir araç ilk kez çağrıldığında app örneğini oluşturur

Parse language code and extract base language and variant. Args: language: The language code, possibly with variant (e.g.

Save data to JSON file

Closes all server connections.

Convert power between units.

Convert pressure between units.

Convert speed between units.

Extract key facts from a Wikipedia article. This is a simplified implementation returning the first few sentences of the summary

Filter a list of mutations. Args: mutations: List of mutation objects with protein_change attribute Returns:

* Calculate the floor of a number * @param number - Number to find the floor of * @returns floor of the number

Generate a hexagram using the traditional three-coin method. Simulates throwing three coins six times to generate six lines,

Get the global endpoint registry.

Fetch variant data from cBioPortal. Args: gene_aa: Gene and AA change format (e.g., "BRAF V600E")

Perform a standalone divination without query integration. Useful for testing the divination system or providing pure I Chin

Record a metric sample. Args: name: Metric name duration: Duration in seconds success: Whether operation

Record a metric to the global collector. Note: This is a no-op if BIOMCP_METRICS_ENABLED is not set to true. Args: name: Metric name

Set item in cache with TTL.

Convert computer storage between units.

Get nix-darwin options matching a specific prefix. Useful for browsing options under a category or finding exact option names. Args:

Augment a user query with bibliomantic I Ching wisdom. This method performs the core bibliomantic operation: 1. Gene

Format a count with appropriate singular/plural label.

Format hexagram information for integration with queries. Args: number: Hexagram number name: Hexagr

Get detailed drug label information by set ID. Args: set_id: Label set ID sections: Specific sections to retrieve (default:

Get a session by ID or the current session.

Inject database links into variant data. Args: variants: List of variant dictionaries from MyVariant.info API Returns:

Check if an exception should trigger a retry. Args: exc: The exception that occurred config: Retry configuration Returns:

Validate if a string is a valid gene symbol. Args: gene: The gene symbol to validate Returns: True if the gene symbol appear

Search for diseases in the NCI CTS database. This provides access to NCI's controlled vocabulary of cancer conditions used in clinical t

Search for interventions in the NCI CTS database. Args: name: Intervention name to search for (partial match) intervention_t

Convert a JSON string or already-parsed data (dict or list) into a simple Markdown representation. :param data: The input data, either as a J

Validate date string format. Args: date_str: Date string in YYYY-MM-DD format Returns: Validated date string or None

Validate and sanitize drug name input. Args: drug: Drug name to validate Returns: Validated drug name or None

Retrieves details for a single article given its identifier. Parameters: - call_benefit: Define and summarize why this function is being

Searches for articles across PubMed and preprint servers. Parameters: - call_benefit: Define and summarize why this function is being ca

Get thread-local database connection

Acquire tokens from the bucket.

Convert area between units.

Convert temperature between units.

Get detailed information about a specific nix-darwin option. Requires an exact option name match. If not found, suggests similar options. Ar

Fetch a single article from Europe PMC by DOI.

Generate enhanced divination with changing lines

Get detailed information for a specific adverse event report. Args: report_id: Safety report ID api_key: Optional OpenFDA AP

Get all registered endpoints. Returns: Dictionary mapping endpoint keys to their metadata

Get a value from cache if not expired.

Get detailed information for a specific device event report. Args: mdr_report_key: MDR report key api_key: Optional OpenFDA

Get disease information from MyDisease.info. Args: disease_id_or_name: Disease ID (MONDO, DOID) or name (e.g., "melanoma", "MONDO:00

Provide statistics about the divination system. Returns: Dictionary containing system information and statistics

Get detailed information about a specific organization. Args: org_id: Organization ID api_key: Optional API key (if not prov

Fetch detailed information for a specific IACR paper Args: paper_id: IACR paper ID (e.g., "2009/101") or full URL

Get a summary of a Wikipedia article. Args: title: The title of the Wikipedia article. Returns:

Fetch variant data from 1000 Genomes via Ensembl.

Map single server name to actual server configuration. Server name should be the local server name (e.g., "National Parks", "DEX Papr

Get statistics about available NixOS flakes. Retrieves statistics from the flake search index including total packages, unique repositories,

Parse OR query into individual search terms. Handles formats like: - "term1 OR term2" - 'term1 OR term2 OR "term with spaces"' - "TER

Dispatch function to handle dict, list, or scalar (str/int/float/bool). :param value: The current JSON data node. :param path_keys: The list

Helper function to run the wikipedia-mcp command and return its output.

Search for biomarkers in the NCI CTS database. Note: Biomarker data availability may be limited per CTRP documentation. Results focus on

Search for organizations in the NCI CTS database. Args: name: Organization name to search for (partial match) org_type: Type

Search for specific mutations across all cBioPortal studies. Args: gene: Gene symbol (e.g., "SRSF2") mutation: Specif

Get a summary of a Wikipedia article tailored to a specific query. This is a simplified implementation that returns a snippet around

Get a summary of a specific section of a Wikipedia article. Args: title: The title of the Wikipedia article.

Add language variant parameter to API request parameters if needed. Args: params: The API request parameters.

Build execution summary for prompt.