BioMCP is a server implementation that provides structured access to key biomedical databases through a unified interface. Developed by GenomOncology, it connects to ClinicalTrials.gov, PubMed (via PubTator3), and MyVariant.info to enable searching and retrieving information about clinical trials, research articles, and genetic variants. The server exposes these capabilities as MCP tools that can be used by AI assistants to access up-to-date biomedical data, overcoming knowledge cutoff limitations. BioMCP handles entity normalization, intelligent rendering of complex data as Markdown, and transparent attribution of sources, making it valuable for biomedical research, clinical decision support, and literature review workflows.
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Highlight AIStart analysis with sequential thinking. Parameters: thought (string), thoughtNumber (int), totalThoughts (int), nextThoughtNeeded (boolean)
Perform a search across biomedical domains. Parameters: query (string), domain (optional string), get_schema (optional boolean), explain_query (optional boolean), genes (optional array), diseases (optional array), conditions (optional array), phase (optional string), significance (optional string)
Retrieve full details for a specified article, trial, or variant. Parameters: domain (string), id (string), detail (optional string)
Search PubMed/PubTator3 and preprints for articles. Parameters: query (string)
Fetch detailed article information. Supports PMID and DOI as parameters: id (string)
Search ClinicalTrials.gov or NCI CTS API for clinical trials. Parameters: conditions (array), phase (optional string), source (optional string), api_key (optional string)
Fetch all trial details from either ClinicalTrials.gov or NCI CTS API. Parameters: id (string)
Fetch protocol information only from ClinicalTrials.gov. Parameters: id (string)
Fetch trial publications from ClinicalTrials.gov. Parameters: id (string)
Fetch outcome measures and results from ClinicalTrials.gov. Parameters: id (string)
Fetch site locations and contacts from ClinicalTrials.gov. Parameters: id (string)
Search MyVariant.info database for genetic variants. Parameters: gene (string), significance (optional string)
Fetch comprehensive variant details. Parameters: id (string)
Search NCI's organization database. Parameters: query (string)
Get organization details by ID from NCI. Parameters: id (string)
Search NCI's intervention database (drugs, devices, procedures). Parameters: query (string)
Get intervention details by ID from NCI. Parameters: id (string)
Search biomarkers used in trial eligibility criteria. Parameters: query (string)
Search NCI's controlled vocabulary of cancer conditions. Parameters: query (string)
Get real-time gene information from MyGene.info. Parameters: gene_id_or_symbol (string)
Get disease definitions and synonyms from MyDisease.info. Parameters: disease_id_or_name (string)
Get drug/chemical information from MyChem.info. Parameters: drug_id_or_name (string)
