Registry

MCP server providing access to a variety of biological resources, including STRINGDb, Open Targets, Reactome, UniProt, Human Protein Atlas, PanglaoDb, grants.gov, EuropePMC, AlphaFold, OLS, Ensembl, Antibody Registry, KEGG, Drugs@openFDA, ClinicalTrials.gov, bioRxiv, Google Scholar, InterPro and PRIDE. Available via `pip`/`uv` as `biocontext_kb`.

The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions.

Exposes STRING database functionality as an MCP (Model Context Protocol) server. This server wraps STRING API endpoints and makes them available as MCP tools for use with AI agents or other MCP-compatible clients.

A unified biomedical graph database that integrates 50+ primary data sources — genes, proteins, compounds, diseases, pathways, and clinical data — into a single queryable graph with billions of cross-reference edges. Its native MCP server gives LLMs direct access to structured, authoritative biomedical data, complementing their reasoning with reliable identifiers and up-to-date database content.

Knowledge curation, grounding, and harmonisation are complex processes. The BioCypher ecosystem (https://biocypher.org) supports the deterministic mapping of diverse inputs to harmonised graphs. To further simplify the creation and maintenance of BioCypher pipelines, we provide an MCP server with implementation guidelines and structured documentation for LLM co-programmers. The remote Streamable HTTP endpoint can be connected to your favourite copilot software, helping with pipeline creation and adapter design and automation.

A Model Context Protocol (MCP) server for searching and accessing RNA sequencing datasets from the European Nucleotide Archive (ENA). Find publicly available bulk RNA-seq and single-cell RNA-seq datasets to validate research hypotheses or reproduce published analyses.

An unofficial Model Context Protocol (MCP) server for the SIB Cellosaurus cell line knowledge resource.

OmniPath integrates data from 150+ resources to provide a comprehensive view of molecular interactions, pathways, and biological annotations. This MCP server enables LLMs to execute SQL queries against the Omnipath database. The tool description includes context about the database schema and some template queries to facilitate accurate query generation.

DisPhaseDB MCP enables AI assistants to directly access biologically data of proteins involved in liquid–liquid phase separation (LLPS), including disease-associated mutations, functional regions and condensate associations.

ToolUniverse is a collection of biomedical tools designed for use by Agentic AI. It is a critical component of TxAgent, providing the agent with the ability to access and leverage a vast array of biomedical knowledge to solve complex therapeutic reasoning tasks. ToolUniverse includes 211 biomedical tools that address various aspects of drugs and diseases.

BioMCP is an open source (MIT License) toolkit that empowers AI assistants and agents with specialized biomedical knowledge. Built following the Model Context Protocol (MCP), it connects AI systems to authoritative biomedical data sources, enabling them to answer questions about clinical trials, scientific literature, and genomic variants with precision and depth.

A set of Model Context Protocol (MCP) servers that provides seamless access to the Protein Data Bank in Europe (PDBe) API and PDBe Graph Database. This server exposes PDBe's comprehensive structural biology data as MCP tools, enabling direct integration with Claude Desktop and other AI-powered applications.

MCP server for spatial transcriptomics analysis through natural language conversation. Unifies 60+ methods across 15 analytical categories spanning Python and R ecosystems, including cell type annotation, spatial domain identification, deconvolution, cell-cell communication, trajectory analysis, and spatial statistics.

MCP (Model Context Protocol) server for Biothings.io

MCP server for remote control of napari viewers via Model Context Protocol (MCP). Perfect for AI-assisted microscopy analysis with Claude Desktop and other LLM applications.

A Model Context Protocol server for the gget bioinformatics library. See details about gget: https://pachterlab.github.io/gget/

Model Context Protocol (MCP) Server providing a robust, developer-friendly interface to the official ClinicalTrials.gov v2 API. Enables LLMs and AI agents to search, retrieve, and analyze clinical study data programmatically.

Provide tools that helps users to access biological data resources from the SIB Swiss Institute of Bioinformatics, such as UniProt, Bgee, Rhea, SwissLipids, through the SPARQL query language.