Fetch all mutations for a gene across all profiles.

Fetch mutations for a gene from mutation profiles. Args: gene_id: Entrez gene ID mutation_profiles: List of molecular

Fetch metadata for a single study.

Fetch study metadata in parallel for cancer type information. Args: study_ids: List of study IDs to fetch Returns:

Filter server configurations based on criteria

Filter mutations by amino acid change. Args: mutations_data: List of mutation records from cBioPortal aa_change: Amin

Fix invalid JSON format from LLM response.

Extract and format address fields from organization data.

Format the header section of detailed approval.

Format a single approval record summary.

Format basic drug information.

Format the header section of biomarker results.

Format biomarker requirements section.

Format boxed warning section.

Format clinical drug information.

Helper method to recursively format comment tree with proper indentation

Format conditions/diseases section.

Format contact information lines.

Format contact information section.

Format detailed metadata from OpenFDA.

Format basic device information.

Format device class and specialty information.

Format individual device information.

Format OpenFDA device data.

Format disease code mappings.

Format disease output for display.

Format disease synonyms section.

Format distribution information.

Format drug information for text output.

Format eligibility criteria section.

Format enhanced consultation with full traditional elements

Format intervention header and basic info.

Format clinical indications section.

Format regulatory information section.

Format intervention synonyms section.

Format interventions section.

Format basic label information from OpenFDA data.

Format key label sections.

Format locations section.

Format a found version for display.

Format a single NixHub release for display.

Format no results message.

Format no results message.

Format OpenFDA metadata.

Format organizations section.

Format patient demographic information.

Format patient impact information.

Format patient information section.

Format AlphaGenome predictions into markdown. Args: variant: The variant object from AlphaGenome scores: List of prediction score

Format product information.

Format protocol information section.

Format summary of recall classifications.

Format recall details and reason.

Format the header section of detailed recall.

Format OpenFDA metadata for recall.

Format a single recall summary.

Format the search summary section.

Format the search summary.

Format detailed shortage information.

Format a single shortage entry.

Format summary of shortage statuses.

Format a single biomarker record.

Format a single disease record.

Format submission history.

Format summary section.

Format tool descriptions for prompt

Format tools for evaluation prompt

Format trial conditions/diseases.

Format trial header with basic info.

Format trial header section.

Format trial interventions.

Format trial metadata (sponsor, eligibility notes).

Format a single trial summary.

Format trial summary text if available.

Retrieves detailed information for a single gene from MyGene.info. This tool provides real-time gene annotations including: - Official g

Stage 2: Generate fuzzy version with evidence requirements

Generate evaluation prompt with randomized structure

Generate reasoning about the evaluation result.

Generate reasoning about the evaluation result.

Generate a single detailed task

Get regex patterns to match amino acid changes. Handles various notation formats: - Direct match (e.g., "V600E") - With p. pr

Get cancer type hierarchy (cached).

Get empty current metrics for when no tasks completed

Get empty model summary for when no tasks completed

Get qwen3-32b as fallback LLM for content filtering issues.

Get the first value from a list or return the value itself.

Get Entrez gene ID from gene symbol. Args: gene: Gene symbol (e.g., "BRAF") Returns: Entrez gene ID if found

Get regular gene cBioPortal summary.

Get relevant mutation profiles for a gene. Args: gene: Gene symbol to find profiles for Returns: List of mut

Get mutation-specific cBioPortal summary.

Get mutation summary across selected profiles.

Generate a key for the connection pool.

Get mutations for a gene in a specific profile.

Get all domains referenced in the query.

Get molecular profiles relevant to the gene.

Get retry configuration based on settings.

Generate a cache key for search requests.