Content
biomcp 35
BioMCP is an open-source toolkit for AI in biomedicine, connecting to reliable data sources.
search
Search biomedical literature, clinical trials, genetic variants, genes, drugs, and diseases. ⚠️ IMPORTANT: Have you used the 'think' tool first? If not, STOP and use it NOW! The 'think' tool is REQUIRED for proper research planning and should be your FIRST step. This tool provides access to biomedical data from PubMed/PubTator3, ClinicalTrials.gov, MyVariant.info, and the BioThings suite (MyGene.info, MyChem.info, MyDisease.info). It supports two search modes: ## 1. UNIFIED QUERY LANGUAGE Use the 'query' parameter with field-based syntax for precise cross-domain searches. Syntax: - Basic: "gene:BRAF" - AND logic: "gene:BRAF AND disease:melanoma" - OR logic: "gene:PTEN AND (R173 OR Arg173 OR 'position 173')" - Domain-specific: "trials.condition:melanoma AND trials.phase:3" Common fields: - Cross-domain: gene, disease, variant, chemical/drug - Articles: pmid, title, abstract, journal, author - Trials: trials.condition, trials.intervention, trials.phase, trials.status - Variants: variants.hgvs, variants.rsid, variants.significance Example: ``` await search( query="gene:BRAF AND disease:melanoma AND trials.phase:3", max_results_per_domain=20 ) ``` ## 2. DOMAIN-SPECIFIC SEARCH Use the 'domain' parameter with specific filters for targeted searches. Domains: - "article": Search PubMed/PubTator3 for research articles and preprints ABOUT genes, variants, diseases, or chemicals - "trial": Search ClinicalTrials.gov for clinical studies - "variant": Search MyVariant.info for genetic variant DATABASE RECORDS (population frequency, clinical significance, etc.) - NOT for articles about variants! - "gene": Search MyGene.info for gene information (symbol, name, function, aliases) - "drug": Search MyChem.info for drug/chemical information (names, formulas, indications) - "disease": Search MyDisease.info for disease information (names, definitions, synonyms) - "nci_organization": Search NCI database for cancer centers, hospitals, and research sponsors (requires API key) - "nci_intervention": Search NCI database for drugs, devices, procedures used in cancer trials (requires API key) - "nci_biomarker": Search NCI database for biomarkers used in trial eligibility criteria (requires API key) - "nci_disease": Search NCI controlled vocabulary for cancer conditions and terms (requires API key) Example: ``` await search( domain="article", genes=["BRAF", "NRAS"], diseases=["melanoma"], page_size=50 ) ``` ## DOMAIN SELECTION EXAMPLES: - To find ARTICLES about BRAF V600E mutation: domain="article", genes=["BRAF"], variants=["V600E"] - To find VARIANT DATA for BRAF mutations: domain="variant", gene="BRAF" - To find articles about ERBB2 p.D277Y: domain="article", genes=["ERBB2"], variants=["p.D277Y"] - Common mistake: Using domain="variant" when you want articles about a variant ## IMPORTANT NOTES: - For complex research questions, use the separate 'think' tool for systematic analysis - The tool returns results in OpenAI MCP format: {"results": [{"id", "title", "text", "url"}, ...]} - Search results do NOT include metadata (per OpenAI MCP specification) - Use the fetch tool to get detailed metadata for specific records - Use get_schema=True to explore available search fields - Use explain_query=True to understand query parsing (unified mode) - Domain-specific searches use AND logic for multiple values - For OR logic, use the unified query language - NEW: Article search keywords support OR with pipe separator: "R173|Arg173|p.R173" - Remember: domain="article" finds LITERATURE, domain="variant" finds DATABASE RECORDS ## RETURN FORMAT: All search modes return results in this format: ```json { "results": [ { "id": "unique_identifier", "title": "Human-readable title", "text": "Summary or snippet of content", "url": "Link to full resource" } ] } ```
NCI API key for searching NCI domains (nci_organization, nci_intervention, nci_biomarker, nci_disease). Required for NCI searches. Get a free key at: https://clinicaltrialsapi.cancer.gov/
Brief explanation of why this search is being performed and expected benefit. Helps improve search accuracy and provides context for analytics. Highly recommended for better results.
Domain to search: 'article' for papers/literature ABOUT genes/variants/diseases, 'trial' for clinical studies, 'variant' for genetic variant DATABASE RECORDS, 'gene' for gene information from MyGene.info, 'drug' for drug/chemical information from MyChem.info, 'disease' for disease information from MyDisease.info, 'nci_organization' for NCI cancer centers/sponsors, 'nci_intervention' for NCI drugs/devices/procedures, 'nci_biomarker' for NCI trial eligibility biomarkers, 'nci_disease' for NCI cancer vocabulary, 'fda_adverse' for FDA adverse event reports, 'fda_label' for FDA drug labels, 'fda_device' for FDA device events, 'fda_approval' for FDA drug approvals, 'fda_recall' for FDA drug recalls, 'fda_shortage' for FDA drug shortages
fetch
Fetch comprehensive details for a specific biomedical record. This tool retrieves full information for articles, clinical trials, genetic variants, genes, drugs, or diseases using their unique identifiers. It returns data in a standardized format suitable for detailed analysis and research. ## IDENTIFIER FORMATS: - Articles: PMID (PubMed ID) - e.g., "35271234" OR DOI - e.g., "10.1101/2024.01.20.23288905" - Trials: NCT ID (ClinicalTrials.gov ID) - e.g., "NCT04280705" - Variants: HGVS notation or dbSNP ID - e.g., "chr7:g.140453136A>T" or "rs121913254" - Genes: Gene symbol or Entrez ID - e.g., "BRAF" or "673" - Drugs: Drug name or ID - e.g., "imatinib" or "DB00619" - Diseases: Disease name or ID - e.g., "melanoma" or "MONDO:0005105" - NCI Organizations: NCI organization ID - e.g., "NCI-2011-03337" - NCI Interventions: NCI intervention ID - e.g., "INT123456" - NCI Diseases: NCI disease ID - e.g., "C4872" The domain is automatically detected from the ID format if not provided: - NCT* → trial - Contains "/" with numeric prefix (DOI) → article - Pure numeric → article (PMID) - rs* or contains ':' or 'g.' → variant - For genes, drugs, diseases: manual specification recommended ## DOMAIN-SPECIFIC OPTIONS: ### Articles (domain="article"): - Returns full article metadata, abstract, and full text when available - Supports both PubMed articles (via PMID) and Europe PMC preprints (via DOI) - Includes annotations for genes, diseases, chemicals, and variants (PubMed only) - detail="full" attempts to retrieve full text content (PubMed only) ### Clinical Trials (domain="trial"): - detail=None or "protocol": Core study information - detail="locations": Study sites and contact information - detail="outcomes": Primary/secondary outcomes and results - detail="references": Related publications and citations - detail="all": Complete trial record with all sections ### Variants (domain="variant"): - Returns comprehensive variant information including: - Clinical significance and interpretations - Population frequencies - Gene/protein effects - External database links - detail parameter is ignored (always returns full data) ### Genes (domain="gene"): - Returns gene information from MyGene.info including: - Gene symbol, name, and type - Entrez ID and Ensembl IDs - Gene summary and aliases - RefSeq information - detail parameter is ignored (always returns full data) ### Drugs (domain="drug"): - Returns drug/chemical information from MyChem.info including: - Drug name and trade names - Chemical formula and structure IDs - Clinical indications - Mechanism of action - External database links (DrugBank, PubChem, ChEMBL) - detail parameter is ignored (always returns full data) ### Diseases (domain="disease"): - Returns disease information from MyDisease.info including: - Disease name and definition - MONDO ontology ID - Disease synonyms - Cross-references to other databases - Associated phenotypes - detail parameter is ignored (always returns full data) ### NCI Organizations (domain="nci_organization"): - Returns organization information from NCI database including: - Organization name and type - Full address and contact information - Research focus areas - Associated clinical trials - Requires NCI API key - detail parameter is ignored (always returns full data) ### NCI Interventions (domain="nci_intervention"): - Returns intervention information from NCI database including: - Intervention name and type - Synonyms and alternative names - Mechanism of action (for drugs) - FDA approval status - Associated clinical trials - Requires NCI API key - detail parameter is ignored (always returns full data) ### NCI Diseases (domain="nci_disease"): - Returns disease information from NCI controlled vocabulary including: - Preferred disease name - Disease category and classification - All known synonyms - Cross-reference codes (ICD, SNOMED) - Requires NCI API key - detail parameter is ignored (always returns full data) ## RETURN FORMAT: All fetch operations return a standardized format: ```json { "id": "unique_identifier", "title": "Record title or name", "text": "Full content or comprehensive description", "url": "Link to original source", "metadata": { // Domain-specific additional fields } } ``` ## EXAMPLES: Fetch article by PMID (domain auto-detected): ``` await fetch(id="35271234") ``` Fetch article by DOI (domain auto-detected): ``` await fetch(id="10.1101/2024.01.20.23288905") ``` Fetch complete trial information (domain auto-detected): ``` await fetch( id="NCT04280705", detail="all" ) ``` Fetch variant with clinical interpretations: ``` await fetch(id="rs121913254") ``` Explicitly specify domain (optional): ``` await fetch( domain="variant", id="chr7:g.140453136A>T" ) ```
NCI API key for fetching NCI records (nci_organization, nci_intervention, nci_disease). Required for NCI fetches. Get a free key at: https://clinicaltrialsapi.cancer.gov/
Brief explanation of why this fetch is being performed and expected benefit. Helps provide context for analytics and improves result relevance.
Domain of the record (auto-detected if not provided)
think
REQUIRED FIRST STEP: Perform structured sequential thinking for ANY biomedical research task. 🚨 IMPORTANT: You MUST use this tool BEFORE any search or fetch operations when: - Researching ANY biomedical topic (genes, diseases, variants, trials) - Planning to use multiple BioMCP tools - Answering questions that require analysis or synthesis - Comparing information from different sources - Making recommendations or drawing conclusions ⚠️ FAILURE TO USE THIS TOOL FIRST will result in: - Incomplete or poorly structured analysis - Missing important connections between data - Suboptimal search strategies - Overlooked critical information Sequential thinking ensures you: 1. Fully understand the research question 2. Plan an optimal search strategy 3. Identify all relevant data sources 4. Structure your analysis properly 5. Deliver comprehensive, well-reasoned results ## Usage Pattern: 1. Start with thoughtNumber=1 to initiate analysis 2. Progress through numbered thoughts sequentially 3. Adjust totalThoughts estimate as understanding develops 4. Set nextThoughtNeeded=False only when analysis is complete ## Example: ```python # Initial analysis await think( thought="Breaking down the relationship between BRAF mutations and melanoma treatment resistance...", thoughtNumber=1, totalThoughts=5, nextThoughtNeeded=True ) # Continue analysis await think( thought="Examining specific BRAF V600E mutation mechanisms...", thoughtNumber=2, totalThoughts=5, nextThoughtNeeded=True ) # Final thought await think( thought="Synthesizing findings and proposing research directions...", thoughtNumber=5, totalThoughts=5, nextThoughtNeeded=False ) ``` ## Important Notes: - Each thought builds on previous ones within a session - State is maintained throughout the MCP session - Use thoughtful, detailed analysis in each step - Revisions and branching are supported through the underlying implementation
Whether more thinking steps are needed after this one
Current thinking step for analysis
Current thought number, starting at 1
Estimated total thoughts needed for complete analysis
article_searcher
Search PubMed/PubTator3 for research articles and preprints. ⚠️ PREREQUISITE: Use the 'think' tool FIRST to plan your research strategy! Use this tool to find scientific literature ABOUT genes, variants, diseases, or chemicals. Results include articles from PubMed and optionally preprints from bioRxiv/medRxiv. Important: This searches for ARTICLES ABOUT these topics, not database records. For genetic variant database records, use variant_searcher instead. Example usage: - Find articles about BRAF mutations in melanoma - Search for papers on a specific drug's effects - Locate research on gene-disease associations
Chemical/drug names to search for
Disease names to search for
Gene symbols to search for
Include cBioPortal cancer genomics summary when searching by gene
Include preprints from bioRxiv/medRxiv
Free-text keywords to search for
Page number (1-based)
Results per page
Variant strings to search for (e.g., 'V600E', 'p.D277Y')
article_getter
Fetch detailed information for a specific article. Retrieves the full abstract and available text for an article by its identifier. Supports: - PubMed IDs (PMID) for published articles - PMC IDs for articles in PubMed Central - DOIs for preprints from Europe PMC Returns formatted text including: - Title - Abstract - Full text (when available from PMC for published articles) - Source information (PubMed or Europe PMC)
Article identifier - either a PubMed ID (e.g., '38768446' or 'PMC11193658') or DOI (e.g., '10.1101/2024.01.20.23288905')
trial_searcher
Search ClinicalTrials.gov for clinical studies. ⚠️ PREREQUISITE: Use the 'think' tool FIRST to plan your research strategy! Comprehensive search tool for finding clinical trials based on multiple criteria. Supports filtering by conditions, interventions, location, phase, and eligibility. Location search notes: - Use either location term OR lat/long coordinates, not both - For city-based searches, AI agents should geocode to lat/long first - Distance parameter only works with lat/long coordinates Returns a formatted list of matching trials with key details.
Filter by age group
Medical conditions to search for
Distance in miles from lat/long coordinates
Filter by funding source
Filter by healthy volunteer eligibility
Treatment interventions to search for
Latitude for location-based search. AI agents should geocode city names before using.
Location term for geographic filtering
Longitude for location-based search. AI agents should geocode city names before using.
Additional search terms
Page number (1-based)
Results per page
Filter by clinical trial phase
Filter by recruiting status
Filter by biological sex
Filter by study type
trial_getter
Fetch comprehensive details for a specific clinical trial. Retrieves all available information for a clinical trial by its NCT ID. This includes protocol details, locations, outcomes, and references. For specific sections only, use the specialized getter tools: - trial_protocol_getter: Core protocol information - trial_locations_getter: Site locations and contacts - trial_outcomes_getter: Primary/secondary outcomes and results - trial_references_getter: Publications and references
NCT ID (e.g., 'NCT06524388')
trial_protocol_getter
Fetch core protocol information for a clinical trial. Retrieves essential protocol details including: - Official title and brief summary - Study status and sponsor information - Study design (type, phase, allocation, masking) - Eligibility criteria - Primary completion date
NCT ID (e.g., 'NCT06524388')
trial_references_getter
Fetch publications and references for a clinical trial. Retrieves all linked publications including: - Published results papers - Background literature - Protocol publications - Related analyses Includes PubMed IDs when available for easy cross-referencing.
NCT ID (e.g., 'NCT06524388')
trial_outcomes_getter
Fetch outcome measures and results for a clinical trial. Retrieves detailed outcome information including: - Primary outcome measures - Secondary outcome measures - Results data (if available) - Adverse events (if reported) Note: Results are only available for completed trials that have posted data.
NCT ID (e.g., 'NCT06524388')
trial_locations_getter
Fetch contact and location details for a clinical trial. Retrieves all study locations including: - Facility names and addresses - Principal investigator information - Contact details (when recruiting) - Recruitment status by site Useful for finding trials near specific locations or contacting study teams.
NCT ID (e.g., 'NCT06524388')
variant_searcher
Search MyVariant.info for genetic variant DATABASE RECORDS. ⚠️ PREREQUISITE: Use the 'think' tool FIRST to plan your research strategy! Important: This searches for variant DATABASE RECORDS (frequency, significance, etc.), NOT articles about variants. For articles about variants, use article_searcher. Searches the comprehensive variant database including: - Population frequencies (gnomAD, 1000 Genomes, etc.) - Clinical significance (ClinVar) - Functional predictions (SIFT, PolyPhen, CADD) - Gene and protein consequences Search by various identifiers or filter by clinical/functional criteria.
Minimum CADD score for pathogenicity
Variant consequence (e.g., 'missense_variant')
Maximum allele frequency
Minimum allele frequency
Gene symbol (e.g., 'BRAF', 'TP53')
HGVS notation (genomic, coding, or protein)
Coding sequence change (e.g., 'c.1799T>A')
Protein change in HGVS format (e.g., 'p.V600E')
Include cBioPortal cancer genomics summary when searching by gene
Include OncoKB precision oncology summary when searching by gene
Page number (1-based)
Results per page
PolyPhen-2 functional prediction
Genomic region (e.g., 'chr7:140753336-140753337')
dbSNP rsID (e.g., 'rs113488022')
SIFT functional prediction
Clinical significance filter
variant_getter
Fetch comprehensive details for a specific genetic variant. Retrieves all available information for a variant including: - Gene location and consequences - Population frequencies across databases - Clinical significance from ClinVar - Functional predictions - External annotations (TCGA cancer data, conservation scores) Accepts various ID formats: - HGVS: NM_004333.4:c.1799T>A - rsID: rs113488022 - MyVariant ID: chr7:g.140753336A>T
Include external annotations (TCGA, 1000 Genomes, functional predictions)
Variant ID (HGVS, rsID, or MyVariant ID like 'chr7:g.140753336A>T')
alphagenome_predictor
Predict variant effects on gene regulation using Google DeepMind's AlphaGenome. ⚠️ PREREQUISITE: Use the 'think' tool FIRST to plan your analysis strategy! AlphaGenome provides state-of-the-art predictions for how genetic variants affect gene regulation, including: - Gene expression changes (RNA-seq) - Chromatin accessibility impacts (ATAC-seq, DNase-seq) - Splicing alterations - Promoter activity changes (CAGE) This tool requires: 1. AlphaGenome to be installed (see error message for instructions) 2. An API key from https://deepmind.google.com/science/alphagenome API Key Options: - Provide directly via the api_key parameter - Or set ALPHAGENOME_API_KEY environment variable Example usage: - Predict regulatory effects of BRAF V600E mutation: chr7:140753336 A>T - Assess non-coding variant impact on gene expression - Evaluate promoter variants in specific tissues Note: This is an optional tool that enhances variant interpretation with AI predictions. Standard annotations remain available via variant_getter.
Alternate allele(s) (e.g., 'T', 'A')
AlphaGenome API key. Check if user mentioned 'my AlphaGenome API key is...' in their message. If not provided here and no env var is set, user will be prompted to provide one.
Chromosome (e.g., 'chr7', 'chrX')
Size of genomic interval to analyze in bp (max 1,000,000)
1-based genomic position of the variant
Reference allele(s) (e.g., 'A', 'ATG')
Threshold for significant log2 fold changes (default: 0.5)
UBERON ontology terms for tissue-specific predictions (e.g., 'UBERON:0002367' for external ear)
gene_getter
Get detailed gene information from MyGene.info. ⚠️ PREREQUISITE: Use the 'think' tool FIRST to understand your research goal! Provides real-time gene annotations including: - Official gene name and symbol - Gene summary/description - Aliases and alternative names - Gene type (protein-coding, etc.) - Links to external databases This tool fetches CURRENT gene information from MyGene.info, ensuring you always have the latest annotations and nomenclature. Example usage: - Get information about TP53 tumor suppressor - Look up BRAF kinase gene details - Find the official name for a gene by its alias Note: For genetic variants, use variant_searcher. For articles about genes, use article_searcher.
Gene symbol (e.g., 'TP53', 'BRAF') or Entrez ID (e.g., '7157')
disease_getter
Get detailed disease information from MyDisease.info. ⚠️ PREREQUISITE: Use the 'think' tool FIRST to understand your research goal! Provides real-time disease annotations including: - Official disease name and definition - Disease synonyms and alternative names - Ontology mappings (MONDO, DOID, OMIM, etc.) - Associated phenotypes - Links to disease databases This tool fetches CURRENT disease information from MyDisease.info, ensuring you always have the latest ontology mappings and definitions. Example usage: - Get the definition of GIST (Gastrointestinal Stromal Tumor) - Look up synonyms for melanoma - Find the MONDO ID for a disease by name Note: For clinical trials about diseases, use trial_searcher. For articles about diseases, use article_searcher.
Disease name (e.g., 'melanoma', 'lung cancer') or ontology ID (e.g., 'MONDO:0016575', 'DOID:1909')
drug_getter
Get detailed drug/chemical information from MyChem.info. ⚠️ PREREQUISITE: Use the 'think' tool FIRST to understand your research goal! This tool provides comprehensive drug information including: - Chemical properties (formula, InChIKey) - Drug identifiers (DrugBank, ChEMBL, PubChem) - Trade names and brand names - Clinical indications - Mechanism of action - Pharmacology details - Links to drug databases This tool fetches CURRENT drug information from MyChem.info, part of the BioThings suite, ensuring you always have the latest drug data. Example usage: - Get information about imatinib (Gleevec) - Look up details for DrugBank ID DB00619 - Find the mechanism of action for pembrolizumab Note: For clinical trials about drugs, use trial_searcher. For articles about drugs, use article_searcher.
Drug name (e.g., 'aspirin', 'imatinib') or ID (e.g., 'DB00945', 'CHEMBL941')
nci_organization_searcher
Search for organizations in the NCI Clinical Trials database. Searches the National Cancer Institute's curated database of organizations involved in cancer clinical trials. This includes: - Academic medical centers - Community hospitals - Industry sponsors - Government facilities - Research networks Requires NCI API key from: https://clinicaltrialsapi.cancer.gov/ IMPORTANT: To avoid API errors, always use city AND state together when searching by location. The NCI API has limitations on broad searches. Example usage: - Find cancer centers in Boston, MA (city AND state) - Search for "MD Anderson" in Houston, TX - List academic organizations in Cleveland, OH - Search by organization name alone (without location)
NCI API key. Check if user mentioned 'my NCI API key is...' in their message. If not provided here and no env var is set, user will be prompted to provide one.
City where organization is located. IMPORTANT: Always use with state to avoid API errors
Organization name to search for (partial match supported)
Type of organization (e.g., 'Academic', 'Industry', 'Government')
Page number (1-based)
Results per page
State/province code (e.g., 'CA', 'NY'). IMPORTANT: Always use with city to avoid API errors
nci_organization_getter
Get detailed information about a specific organization from NCI. Retrieves comprehensive details about an organization including: - Full name and aliases - Address and contact information - Organization type and role - Associated clinical trials - Research focus areas Requires NCI API key from: https://clinicaltrialsapi.cancer.gov/ Example usage: - Get details about a specific cancer center - Find contact information for trial sponsors - View organization's trial portfolio
NCI API key. Check if user mentioned 'my NCI API key is...' in their message. If not provided here and no env var is set, user will be prompted to provide one.
NCI organization ID (e.g., 'NCI-2011-03337')
nci_intervention_searcher
Search for interventions in the NCI Clinical Trials database. Searches the National Cancer Institute's curated database of interventions used in cancer clinical trials. This includes: - FDA-approved drugs - Investigational agents - Medical devices - Surgical procedures - Radiation therapies - Behavioral interventions Requires NCI API key from: https://clinicaltrialsapi.cancer.gov/ Example usage: - Find all trials using pembrolizumab - Search for CAR-T cell therapies - List radiation therapy protocols - Find dietary interventions
NCI API key. Check if user mentioned 'my NCI API key is...' in their message. If not provided here and no env var is set, user will be prompted to provide one.
Type of intervention: 'Drug', 'Device', 'Biological', 'Procedure', 'Radiation', 'Behavioral', 'Genetic', 'Dietary', 'Other'
Intervention name to search for (e.g., 'pembrolizumab')
Page number (1-based)
Results per page. If not specified, returns all matching results.
Include synonym matches in search
nci_intervention_getter
Get detailed information about a specific intervention from NCI. Retrieves comprehensive details about an intervention including: - Full name and synonyms - Intervention type and category - Mechanism of action (for drugs) - FDA approval status - Associated clinical trials - Combination therapies Requires NCI API key from: https://clinicaltrialsapi.cancer.gov/ Example usage: - Get details about a specific drug - Find all trials using a device - View combination therapy protocols
NCI API key. Check if user mentioned 'my NCI API key is...' in their message. If not provided here and no env var is set, user will be prompted to provide one.
NCI intervention ID (e.g., 'INT123456')
nci_biomarker_searcher
Search for biomarkers in the NCI Clinical Trials database. Searches for biomarkers used in clinical trial eligibility criteria. This is essential for precision medicine trials that select patients based on specific biomarker characteristics. Biomarker examples: - Gene mutations (e.g., BRAF V600E, EGFR T790M) - Protein expression (e.g., PD-L1 ≥ 50%, HER2 positive) - Gene fusions (e.g., ALK fusion, ROS1 fusion) - Other molecular markers (e.g., MSI-H, TMB-high) Requires NCI API key from: https://clinicaltrialsapi.cancer.gov/ Note: Biomarker data availability may be limited in CTRP. Results focus on biomarkers used in trial eligibility criteria. Example usage: - Search for PD-L1 expression biomarkers - Find trials requiring EGFR mutations - Look up biomarkers tested by NGS - Search for HER2 expression markers
NCI API key. Check if user mentioned 'my NCI API key is...' in their message. If not provided here and no env var is set, user will be prompted to provide one.
Type of biomarker ('reference_gene' or 'branch')
Biomarker name to search for (e.g., 'PD-L1', 'EGFR mutation')
Page number (1-based)
Results per page
nci_disease_searcher
Search NCI's controlled vocabulary of cancer conditions. Searches the National Cancer Institute's curated database of cancer conditions and diseases used in clinical trials. This is different from the general disease_getter tool which uses MyDisease.info. NCI's disease vocabulary provides: - Official cancer terminology used in trials - Disease synonyms and alternative names - Hierarchical disease classifications - Standardized disease codes for trial matching Requires NCI API key from: https://clinicaltrialsapi.cancer.gov/ Example usage: - Search for specific cancer types (e.g., "melanoma") - Find all lung cancer subtypes - Look up official names for disease synonyms - Get standardized disease terms for trial searches Note: This is specifically for NCI's cancer disease vocabulary. For general disease information, use the disease_getter tool.
NCI API key. Check if user mentioned 'my NCI API key is...' in their message. If not provided here and no env var is set, user will be prompted to provide one.
Disease category/type filter
Include synonym matches in search
Disease name to search for (partial match)
Page number (1-based)
Results per page
openfda_adverse_searcher
Search FDA adverse event reports (FAERS) for drug safety information. ⚠️ PREREQUISITE: Use the 'think' tool FIRST to plan your research strategy! Searches FDA's Adverse Event Reporting System for: - Drug side effects and adverse reactions - Serious event reports (death, hospitalization, disability) - Safety signal patterns across patient populations Note: These reports do not establish causation - they are voluntary reports that may contain incomplete or unverified information.
Optional OpenFDA API key (overrides OPENFDA_API_KEY env var)
Drug name to search for adverse events
Maximum number of results
Page number (1-based)
Adverse reaction term to search for
Filter for serious events only
openfda_adverse_getter
Get detailed information for a specific FDA adverse event report. Retrieves complete details including: - Patient demographics and medical history - All drugs involved and dosages - Complete list of adverse reactions - Event narrative and outcomes - Reporter information
Optional OpenFDA API key (overrides OPENFDA_API_KEY env var)
Safety report ID
openfda_label_searcher
Search FDA drug product labels (SPL) for prescribing information. ⚠️ PREREQUISITE: Use the 'think' tool FIRST to plan your research strategy! Searches official FDA drug labels for: - Approved indications and usage - Dosage and administration guidelines - Contraindications and warnings - Drug interactions and adverse reactions - Special population considerations Label sections include: indications, dosage, contraindications, warnings, adverse, interactions, pregnancy, pediatric, geriatric, overdose
Optional OpenFDA API key (overrides OPENFDA_API_KEY env var)
Filter for drugs with boxed warnings
Search for drugs indicated for this condition
Maximum number of results
Drug name to search for
Page number (1-based)
Specific label section (e.g., 'contraindications', 'warnings')
openfda_label_getter
Get complete FDA drug label information by set ID. Retrieves the full prescribing information including: - Complete indications and usage text - Detailed dosing instructions - All warnings and precautions - Clinical pharmacology and studies - Manufacturing and storage information Specify sections to retrieve specific parts, or leave empty for default key sections.
Optional OpenFDA API key (overrides OPENFDA_API_KEY env var)
Specific sections to retrieve (default: key sections)
Label set ID
openfda_device_searcher
Search FDA device adverse event reports (MAUDE) for medical device issues. ⚠️ PREREQUISITE: Use the 'think' tool FIRST to plan your research strategy! Searches FDA's device adverse event database for: - Device malfunctions and failures - Patient injuries related to devices - Genomic test and diagnostic device issues By default, filters to genomic/diagnostic devices relevant to precision medicine. Set genomics_only=False to search all medical devices.
Optional OpenFDA API key (overrides OPENFDA_API_KEY env var)
Device name to search for
Filter to genomic/diagnostic devices only
Maximum number of results
Manufacturer name
Page number (1-based)
Device problem description
FDA product code
openfda_device_getter
Get detailed information for a specific FDA device event report. Retrieves complete device event details including: - Device identification and specifications - Complete event narrative - Patient outcomes and impacts - Manufacturer analysis and actions - Remedial actions taken
Optional OpenFDA API key (overrides OPENFDA_API_KEY env var)
MDR report key
openfda_approval_searcher
Search FDA drug approval records from Drugs@FDA database. ⚠️ PREREQUISITE: Use the 'think' tool FIRST to plan your research strategy! Returns information about: - Application numbers and sponsors - Brand and generic names - Product formulations and strengths - Marketing status and approval dates - Submission history Useful for verifying if a drug is FDA-approved and when.
Optional OpenFDA API key (overrides OPENFDA_API_KEY env var)
NDA or BLA application number
Year of approval (YYYY format)
Drug name (brand or generic) to search for
Maximum number of results
Page number (1-based)
openfda_approval_getter
Get detailed FDA drug approval information for a specific application. Returns comprehensive approval details including: - Full product list with dosage forms and strengths - Complete submission history - Marketing status timeline - Therapeutic equivalence codes - Pharmacologic class information
Optional OpenFDA API key (overrides OPENFDA_API_KEY env var)
NDA or BLA application number
openfda_recall_searcher
Search FDA drug recall records from the Enforcement database. ⚠️ PREREQUISITE: Use the 'think' tool FIRST to plan your research strategy! Returns recall information including: - Classification (Class I, II, or III) - Recall reason and description - Product identification - Distribution information - Recalling firm details - Current status Class I = most serious (death/serious harm) Class II = moderate (temporary/reversible harm) Class III = least serious (unlikely to cause harm)
Optional OpenFDA API key (overrides OPENFDA_API_KEY env var)
Drug name to search for recalls
Maximum number of results
Page number (1-based)
Search text in recall reason
Recall classification (1=most serious, 2=moderate, 3=least serious)
Show recalls after this date (YYYYMMDD format)
Recall status (ongoing, completed, terminated)
openfda_recall_getter
Get detailed FDA drug recall information for a specific recall. Returns complete recall details including: - Full product description and code information - Complete reason for recall - Distribution pattern and locations - Quantity of product recalled - Firm information and actions taken - Timeline of recall events
Optional OpenFDA API key (overrides OPENFDA_API_KEY env var)
FDA recall number
openfda_shortage_searcher
Search FDA drug shortage records. ⚠️ PREREQUISITE: Use the 'think' tool FIRST to plan your research strategy! Returns shortage information including: - Current shortage status - Shortage start and resolution dates - Reason for shortage - Therapeutic category - Manufacturer information - Estimated resolution timeline Note: Shortage data is cached and updated periodically. Check FDA.gov for most current information.
Optional OpenFDA API key (overrides OPENFDA_API_KEY env var)
Drug name (generic or brand) to search
Maximum number of results
Page number (1-based)
Shortage status (current or resolved)
Therapeutic category (e.g., Oncology, Anti-infective)
openfda_shortage_getter
Get detailed FDA drug shortage information for a specific drug. Returns comprehensive shortage details including: - Complete timeline of shortage - Detailed reason for shortage - All affected manufacturers - Alternative products if available - Resolution status and estimates - Additional notes and recommendations Data is updated periodically from FDA shortage database.
Optional OpenFDA API key (overrides OPENFDA_API_KEY env var)
Drug name (generic or brand)
awesome-mcp-servers
git
Appwrite
TrendRadar
oh-my-opencode
