"A tool that can connect to MySQL database, understand table structure and query related data" matching MCP servers:

Enables AI assistants to query the Ubergraph biomedical ontology SPARQL endpoint with tools for custom SPARQL queries, term lookup, search, and hierarchy traversal.

Provides an MCP interface to the ROBOT command-line tool for OWL ontology editing, enabling operations like merging, reasoning, and conversion via natural language.

Searches UniProt by protein name to find accession numbers and retrieves detailed protein structure information from AlphaFold, including direct links to 3D structural predictions.

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.

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.

MCP server that provides tools to query harmonized gene-disease validity data from the Gene Curation Coalition, supporting consensus and conflict detection for gene-disease assertions.

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.

A Model Context Protocol (MCP) server for interacting with Gen3 data commons, with GraphQL query validation to reduce hallucinations.

Renders interactive 2D molecular structure diagrams from SMILES notation and computes molecular properties like molecular weight, LogP, and TPSA, directly in the chat.

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.

A Model Context Protocol server that interfaces with Biomart databases, allowing models to discover biological datasets, explore attributes/filters, retrieve biological data, and translate between different biological identifiers.

An MCP server that provides mouse genetics data from Mouse Genome Informatics (MGI), enabling LLM agents to query markers, mutations, alleles, phenotypes, and disease models.

A bridge connecting AI agents to NCBI's PubMed database through the Model Context Protocol, enabling seamless searching, retrieval, and analysis of biomedical literature and data.

Enables LLM agents to search biomedical literature, retrieve article details, find related papers, manage caching, and download open-access full texts through MCP with structured, agent-friendly responses.

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.

Provides access to EMBL-EBI bioinformatics data including InterPro domains, Pfam families, protein features, and taxonomy through a unified tool.

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.