Build Essie fragment for line of therapy.

Build planning prompt.

Build Essie fragments for prior therapy search.

Estimate token count using character-based approximation.

Get shortage data from cache if valid, otherwise fetch new data. Returns: Dictionary with shortage data or None if unavailable

Get disease details by ID from MyDisease.info.

Get drug details by ID from MyChem.info.

Get gene details by ID from MyGene.info.

Inject NCT IDs into params using intersection or id-only semantics. Args: params: The parameter dictionary to modify ids: List of

Run benchmark across multiple models for current task file

Summarize content using LLM to keep it under threshold tokens.

Retrieves core protocol information for a single clinical trial identified by its NCT ID. Parameters: - call_benefit: Define and sum

Internal unified search implementation. Parses the unified query language and routes to appropriate domain tools. Supports field-based syntax

Make HTTP request with optional retry logic. Args: method: HTTP method (GET or POST) url: Target URL params: Request para

Clear all cached entries.

Compress accumulated_information using LLM to reduce token usage Args: target_tokens: Target token count

Connects to all configured servers and discovers their tools.

Convert length between units.

Convert volume between units.

Format cBioPortal search summary for display.

Calculate summary statistics from samples.

Generate markdown documentation of all endpoints.

Get the full content of a Wikipedia article. Args: title: The title of the Wikipedia article. Return

Get or create a circuit breaker. Args: name: Circuit breaker name config: Configuration (used only on creation) Returns:

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

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

Get summary statistics for a metric. Args: name: Metric name Returns: Summary statistics or None if metric n

Check if the identifier is a DOI.

Check if the identifier is a PubMed ID.

Context manager for rate limiting.

* Find the maximum value in an array of numbers * @param numbers - Array of numbers to find the maximum of * @returns The maximum value

Search for interventions in the NCI Clinical Trials database. Searches the National Cancer Institute's curated database of interventions used

Search for organizations in the NCI Clinical Trials database. Searches the National Cancer Institute's curated database of organizations invo

* Run the server

Search across preprint sources and merge results.

Stops the HTTP MCP server process and ensures port is released.

Test a specific MCP tool

Validate if a channel exists and is accessible.

Validate FDA API response structure. Args: response: The FDA API response dictionary required_fields: List of required top-l

Build Essie fragments for biomarker expression requirements.

Build Essie fragment for brain metastases filter.

Ensure the URL section exists in the variant.

Extract sections recursively. Args: sections: The sections to extract. level: The current section level.

Format a generated task into standard structure

Generate a unique cache key for an API request. Args: endpoint: The API endpoint URL params: Query parameters Returns:

Parse search results from JSON strings.

Query MyDisease.info for a disease name.

Query MyChem.info for a drug name.

Query MyGene.info for a gene symbol.

Retrieves contact and location details for a single clinical trial identified by its NCT ID. Parameters: - call_benefit: Define and

Retrieves outcome measures, results (if available), and adverse event data for a single clinical trial. Parameters: - call_benefit:

Retrieves publications and other references associated with a single clinical trial identified by its NCT ID. Parameters: - call_ben

Add a thought to the session.

Analyze tool response for key information.

Check if compression is allowed (only once per execution).

Check if we can start a new round.

Check if we can retry the entire task.

Clear all sessions.

Convert time between timezones

Discovers all available tools and their capabilities from the server (STDIO mode).

* Ensure the icons data is loaded

Extract drug names from an OpenFDA result.

Fetch the text of a list of PubMed IDs.

Filter out specified paths from variant data. Args: variants: List of variant dictionaries from MyVariant.info API Returns:

Format enhanced annotations for display.

Format intervention details as markdown. Args: intervention: Intervention data dictionary Returns: Formatted markdown s

Format organization details as markdown. Args: org: Organization data dictionary Returns: Formatted markdown string

Get a connection pool for the current event loop.

Get current time in specified timezone

Get disease information from MyDisease.info. Args: disease_id_or_name: Disease ID (MONDO, DOID) or name fields: Optio

Get disease synonyms for query expansion. Args: disease_id_or_name: Disease ID or name Returns: List of syno

Get endpoints filtered by category. Args: category: The category to filter by Returns: Dictionary of endpoin

Get gene information from MyGene.info. Args: gene_id_or_symbol: Gene ID (Entrez, Ensembl) or symbol (e.g., "TP53", "7157") o

Get detailed information about a specific intervention. Args: intervention_id: Intervention ID api_key: Optional API key (if

Fetch detailed information for a specific Semantic Scholar paper Args: paper_id (str): Paper identifier in one of the fo

Get topics related to a Wikipedia article based on links and categories. Args: title: The title of the Wikipedia article.

Get trial details from either ClinicalTrials.gov or NCI CTS API. Args: nct_id: NCT identifier (e.g., "NCT04280705") source:

Get all unique domains accessed by BioMCP. Returns: Set of unique domain names (e.g., 'api.ncbi.nlm.nih.gov')

Get variant details from MyVariant.info using the variant identifier. The identifier can be a full HGVS-style string (e.g. "chr7:g.140453136

Infer context from query content

Mark that compression has been performed.

두 값의 가중 평균 계산 Parameters: ----------- a : float 첫 번째 값 b : float 두 번째 값 weight : float 가중치(0~1)

두 값의 가중 평균 계산 Parameters: ----------- a : float 첫 번째 값 b : float 두 번째 값 weight : float 가중치(0~1)

* Calculate the arithmetic mean (average) of an array of numbers * @param numbers - Array of numbers to calculate the mean of * @returns The

Normalize phase values for clinical trials. Converts various formats to standard enum values: - "Phase 3" -> "PHASE3" - "phas

Parse a vector field string into a Sympy Vector. Args: f_str (str): e.g. "[z, -y, x]". x_coord, y_coord, z_coord: optional s

Enhanced simple divination with backward compatibility

Search Europe PMC for preprints with pagination support.

Search for clinical trials using either ClinicalTrials.gov or NCI CTS API. Args: query: TrialQuery object with search parameters

Set a value in cache with TTL.