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npx @modelcontextprotocol/inspector uv run --with biomcp-python biomcp run{
"mcpServers": {
"biomcp": {
"command": "uv",
"args": ["run", "--with", "biomcp-python", "biomcp", "run"]
}
}
}thinkBreaks down complex biomedical queries into sequential steps.
Purely a planning tool with no external interaction.
searchSearches across various biomedical databases using a unified query language or domain-specific filters.
Read-only access to indexed data; no data modification.
fetchRetrieves detailed information for a specific article, trial, or variant.
Retrieves existing data; no modification or creation.
article_searcherSearches PubMed/PubTator3 and preprint servers for biomedical articles.
Read-only access to article databases.
article_getterFetches detailed information for a specific article using PMID or DOI.
Read-only access to article details.
trial_searcherSearches ClinicalTrials.gov or NCI CTS API for clinical trials.
Read-only access to trial databases.
trial_getterFetches all details for a specific clinical trial from either source.
Read-only access to trial details.
trial_protocol_getterFetches protocol information only for a specific clinical trial.
Read-only access to trial protocols.
trial_references_getterFetches publications related to a specific clinical trial.
Read-only access to trial references.
trial_outcomes_getterFetches outcome measures and results for a specific clinical trial.
Read-only access to trial outcomes.
trial_locations_getterFetches site locations and contact information for a specific clinical trial.
Read-only access to trial locations.
variant_searcherSearches the MyVariant.info database for genetic variants.
Read-only access to variant data.
variant_getterFetches comprehensive details for a specific genetic variant.
Read-only access to variant details.
nci_organization_searcherSearches NCI's organization database.
Read-only access to organization data.
nci_organization_getterGets organization details by ID from NCI's database.
Read-only access to organization details.
nci_intervention_searcherSearches NCI's intervention database (drugs, devices, procedures).
Read-only access to intervention data.
nci_intervention_getterGets intervention details by ID from NCI's database.
Read-only access to intervention details.
nci_biomarker_searcherSearches biomarkers used in trial eligibility criteria.
Read-only access to biomarker data.
nci_disease_searcherSearches NCI's controlled vocabulary of cancer conditions.
Read-only access to disease data.
gene_getterGets real-time gene information from MyGene.info.
Read-only access to gene information.
disease_getterGets disease definitions and synonyms from MyDisease.info.
Read-only access to disease definitions.
drug_getterGets drug/chemical information from MyChem.info.
Read-only access to drug information.
BioMCP is generally safe for read-only access to biomedical data. Risks are primarily associated with data interpretation and reliance on external APIs. It's crucial to validate results and ensure responsible use of sensitive information.