BioMCP is an open-source toolkit that connects AI assistants to authoritative biomedical data sources for advanced research.
Sequential thinking tool for breaking down complex biomedical problems systematically. MUST be used first for any biomedical research task.
Unified search tool supporting both natural language queries and structured field syntax for cross-domain biomedical searches across articles, trials, and variants.
Retrieve full details for a single article, trial, or variant using their respective IDs (PMID, DOI, NCT number, or variant ID).
Search PubMed/PubTator3 and preprint servers for biomedical literature with entity annotations.
Fetch detailed article information using PMID or DOI, with optional full-text retrieval.
Search clinical trials from ClinicalTrials.gov or NCI Clinical Trials Search API with advanced filtering options.
Fetch comprehensive trial details from either ClinicalTrials.gov or NCI database.
Retrieve protocol information specifically from ClinicalTrials.gov trials.
Fetch trial-related publications and references from ClinicalTrials.gov.
Retrieve outcome measures and results data from ClinicalTrials.gov trials.
Fetch site locations and contact information for ClinicalTrials.gov trials.
Search MyVariant.info database for genetic variant information with significance filtering.
Fetch comprehensive variant details including TCGA, 1000 Genomes, and cBioPortal annotations.
Search NCI's organization database for cancer research institutions and centers.
Retrieve detailed organization information by NCI organization ID.
Search NCI's intervention database for drugs, devices, and medical procedures used in cancer trials.
Fetch detailed intervention information by NCI intervention ID.
Search biomarkers used in clinical trial eligibility criteria through NCI database.
Search NCI's controlled vocabulary of cancer conditions and disease terms.
Retrieve real-time gene information from MyGene.info including official names, summaries, and database links.
Get disease definitions and synonyms from MyDisease.info for condition expansion in searches.
Fetch drug and chemical compound information from MyChem.info including properties and annotations.
Search FDA Adverse Event Reporting System (FAERS) for post-market drug safety reports.
Search FDA drug labels (SPL) for official prescribing information and regulatory data.
{
"mcpServers": {
"biomcp": {
"command": "uv",
"args": ["run", "--with", "biomcp-python", "biomcp", "run"]
}
}
}