"Accessing and Viewing Data in a MariaDB Database" matching MCP servers:

Enables AI agents to retrieve and analyze breeding data from BrAPI-compliant databases through shared tools, with human-in-the-loop approval and verification.

This server enables multi-agent conversations for interacting with Cirro's biological data platform through its OpenAPI interface, auto-generated using AG2's MCP builder.

MCP server for the STRING protein–protein interaction database, hosted by STRING at mcp.string-db.org. Adapted for LLM grounding: responses are size-limited and include metadata and notes on interpretation and next steps. Tools cover identifier resolution, interaction networks and evidence, functional and PPI enrichment, and sequence similarity search.

Parses MS-DIAL binary lipidomics outputs and runs standard analyses server-side, returning compact summaries so an LLM can drive full lipidomics analysis without exposing raw matrices.

Enables genomic sequence analysis through the Evo 2 model, supporting DNA sequence scoring, embedding, generation, and variant effect prediction with multiple model checkpoints (7B, 40B, 1B parameters).

Enables variant annotation and effect prediction using the Ensembl VEP API, with support for batch and single queries.

MCP server providing access to the BERtron API for aggregating genomic and environmental data from multiple BER data sources, enabling geospatial search and health checks.

Provides direct SQL access to a locally hosted Reactome database, enabling schema discovery, guarded read-only queries, and ergonomic helpers over the full relational schema.

Enables analysis of bulk RNA-seq data using natural language queries, executing R and Python in a Docker container with automatic sample anonymization and privacy controls.

An MCP server for searching and accessing RNA sequencing datasets from the European Nucleotide Archive (ENA), supporting bulk, single-cell, and spatial transcriptomics with advanced filtering and download capabilities.

MCP server that provides tools for querying the Human Phenotype Ontology (HPO) including term lookup, hierarchy exploration, cross-ontology mappings, and gene-phenotype-disease associations, all grounded in a local SQLite database for fast offline lookups.

An MCP server that provides tools for searching and fetching protein data from the UniProt database using the unipressed library.

Enables querying the WormBase database for C. elegans and nematode genomics data, including gene information, protein sequences, phenotypes, interactions, and expression patterns through natural language.

Enables AI agents and applications to search, retrieve, and analyze chemical compounds, substances, and bioassays from PubChem's vast chemical information database through comprehensive tools for chemical research and discovery.

Provides a Model Context Protocol server for accessing and querying biomedical data from BioThings services, including gene, variant, chemical, and taxon annotations.

A Model Context Protocol server providing LLMs with access to the Ensembl genomics database, enabling AI assistants to query gene information, sequences, variants, and other genomic data across multiple species.

Provides standardized access to aging and longevity research data from the OpenGenes database, enabling AI assistants to query comprehensive biomedical datasets through SQL and structured interfaces.

Provides a programmatic interface to the Genome Aggregation Database (gnomAD) API across versions v2.1.1, v3.1.2, and v4.1.0. It enables users to query gene metadata, variant information, population frequencies, and ClinVar data through a unified schema.

Provides seamless access to UniProtKB protein database, enabling queries for protein entries, sequences, Gene Ontology annotations, full-text search, and ID mapping across 200+ database types.

A comprehensive Model Context Protocol (MCP) server that provides access to the AlphaFold Protein Structure Database through a rich set of tools and resources for protein structure prediction analysis.