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

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

Get trademark information by registration number. Args: registration_number: Trademark registration number (e.g., "56789

Get trademark information by serial number. Args: serial_number: Trademark serial number (e.g., "87654321") Ret

Fetch variant data from 1000 Genomes via Ensembl.

MCP Endpoint: List available tools.

Load population assignments from a CSV or infer from sample IDs. The CSV should have columns: sample_id, population If no map is provided, in

Parse effect size from GWAS data, handling both beta and OR formats. Args: beta_str: Beta coefficient as string or_str: Odds

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

Parse VCF using cyvcf2 (faster C-based parser). Falls back to pure Python. Args: vcf_path: Path to VCF file max_variants: Ma

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

Make a rate-limited request to PubChem API. Args: url: Request URL method: HTTP method ('GET' or 'POST') **kwargs: A

Reload all documents from disk.

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

Print summary statistics for all resources.

Convert variants to a pandas DataFrame for analysis. Args: variants: List of VariantRecord sample: Specific sample for VAF/d

Write a list of dicts as CSV.

Build Essie fragment for line of therapy.

Build Essie fragments for prior therapy search.

Render the recommendation cell from enrichment data.

Render the Evidence Level column: badge + checkmark.

Format resources for inclusion in the prompt.

Recursively format a value based on its type and formatting options. Parameters ---------- value: The value to format

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.

Convert headers dict to JSON string for request_api. Returns: JSON string representation of headers.

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

Load DDInter datasets from pickle files, processing if needed. Parameters ---------- data_lake_path : str Path to data lake

Build a ClinPGxClient with all API methods mocked.

Generate a placeholder section for a skill that hasn't been run.

Parse XML fragment and return list of imported nodes. Args: xml_content: String containing XML fragment Returns

Standardize drug names for consistent matching during processing.

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

Apply structural alert filters.

Batch annotate variants using ToolUniverse databases. Args: tu: ToolUniverse instance (loaded) variants: List of VariantReco

Calculate an individual's polygenic risk score from their genotypes. Args: prs_weights: PRSResult object with SNP weights (from buil

Calculate comprehensive molecular properties. Args: smiles: Valid SMILES string Returns: MolecularP

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

Clear all cached entries.

Compare enzyme properties across different organisms.

Compute basic descriptive statistics.

Fraction of possible pairwise FST values actually computed.

Fraction of continental groups represented (out of 7).

Compute observed and expected heterozygosity per population. Observed Het = fraction of heterozygous genotypes (per site, averaged) Expected

Convert odds ratio to beta coefficient (log-odds). Args: odds_ratio: Odds ratio from case-control GWAS Returns: Beta co

Generate new PLAN, overwrite previous PLAN.json, and save old plan and step outputs to history.

Extract key fields from a gene API response.

Extract sample metadata from filepath. Args: filepath: Path to sequencing file Returns: Dict with: sample, patient, lan

Find drug element by DrugBank ID Args: drugbank_id: DrugBank ID (e.g., 'DB00001') Returns: XML elem

Flatten nested list to 1D array.

Format cBioPortal search summary for display.

Calculate summary statistics from samples.

Generate a response from the LLM.

Generate markdown documentation of all endpoints.

Generates a clinical report draft using RuntimeLLMAdapter.

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

Return list of skill names that have results in the profile.

Get all fine-mapped credible sets for a specific GWAS study. Parameters ---------- study_id : str GWAS study accession ID (e

Find and load the CSV data file for a BixBench project.

Get a free port for testing.

Summarize study quality metrics.

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

Suggest experimental validation strategies based on fine-mapping results.

Get value from 2D field with bounds checking.

Infer the type of transformation based on substrate and product.

Insert before with automatic attribute injection.

Check if the identifier is a DOI.

Check if the identifier is a PubMed ID.

Context manager for rate limiting.

Load and display current outputs: 1) {id}_PLAN.json 2) The maximum step number corresponding to {id}_Step_{step_number}.sh 3) Corresp

Merge GWAS associations from GWAS Catalog and Open Targets.

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

Paginate through all results. Args: endpoint: API endpoint params: Query parameters max_results:

Parse a BRENDA reaction entry into structured data.