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

Format sample groups as a readable table.

Build a self-contained HTML report using HtmlReportBuilder.

Convert DataFrame to LaTeX table code. Returns: String with LaTeX table code

Get patent application data by application number. Args: application_number: Application number (e.g., "16123456")

Get genome cache directory.

Get clinical annotations filtered by gene and/or drug.

Get a connection pool for the current event loop.

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 local path to genome if installed.

Get all drug-drug interactions Args: drugbank_id: DrugBank ID Returns: List of interaction dictiona

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

Generate Morgan fingerprint (ECFP). ECFP4 = radius 2, ECFP6 = radius 3

Fetch PheWAS associations from Biobank Japan PheWeb (GRCh37 coords).

Get chemical properties Args: drugbank_id: DrugBank ID Returns: Dictionary with 'calculated' and 'e

Get metadata for a specific PGS score. Returns dict with score metadata including trait, variant count, etc.

Retrieve sequence by Ensembl ID. Args: ensembl_id: Ensembl identifier seq_type: Sequence type ('genomic', 'c

Calculate quality metrics for a GWAS study. Args: study: StudyMetadata object Returns: Dictionary of quality metrics

Get substrate specificity data for an enzyme.

Get transaction history for an application. Args: application_number: Application number Returns: L

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')

Group SRA runs by library type and layout. Returns dict with group names as keys and info dicts as values: { 'RNA-Seq:PAIRED': {

Interpret PRS by converting to percentile and risk category. Args: prs_result: PRSResult with standardized_score calculated

Check if genome is installed locally.

List all skill directories that contain a SKILL.md.

List all notebooks, optionally filtering by archived status.

Get list of all available tasks

List available templates.

Load campaign state from config directory.

Load JSON file and return contents.

Record test result.

Log the prompt and completion to a file.

Merge overlapping regions in the list.

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

Parse timeframe string to start and end days. Examples: "Week 1-4" -> (0, 28), "Month 3" -> (60, 90)

Calculate parsimony informative sites. Returns: (pi_sites_count, alignment_length, pi_percentage)

Query drug adverse events.

Record a test result.

Perform image registration. Args: fixed_image: Reference (fixed) image moving_image: Image to be registered

Resolve genome ID from name or alias.

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

Run full genome comparison pipeline.

Search Europe PMC for preprints with pagination support.

Search for preprints within a date range. Args: start_date: Start date in YYYY-MM-DD format end_date: End da

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

Search works with filters. Args: search: Full-text search query filter_params: Dictionary of filter paramete

Cache response data.

Set a value in cache with TTL.

Setup the registration method with specified parameters. Args: transform: Transform object metric: Similarit

Compute SHA-256 checksum of a file.

Split a 4D NIfTI file into separate modality files for nnUNet Args: input_file: Path to the 4D NIfTI file out

Update the system prompt with the selected resources.

Upload a file attachment to an entry

Write CSV tables from merged results.

Add credible sets from Open Targets for a gene (via its SNPs).

Apply timeout wrapper to all tool functions using multiprocessing.

Add a single comment to commentsExtended.xml.

Add a single comment to commentsExtensible.xml.

Add a single comment to commentsIds.xml.

Add a single comment to comments.xml.

Simple linear regression slope to detect trend direction.

Map a percentile (0-100) to a risk category label.

Calculate exact binomial confidence interval (Clopper-Pearson method). Returns: Lower and upper bounds as percentages

Build Essie fragments for excluded mutations.

Build Essie fragments for progression on therapy search.

Build Essie fragments for required mutations.

Build a table row with Drug, Evidence, Recommendation, Class, Genes.

Build Open Targets variant ID: chr_pos_ref_alt.

Capture any matplotlib plots that might have been generated during execution.