"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.

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

Enables AI agents to retrieve cited pharmacogenomic and gene-variant information, including drug–gene guidance from CPIC/DPWG and rsID lookups, so responses can quote curated sources instead of relying on memory. A local package also lets users read raw DNA files on their own computer without sending the file data to the remote service.

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.

Guides researchers, including those new to BPP, from raw sequence data to a validated control file that has passed a short test run. Wraps BPP command-line tools without running long analyses itself.

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.

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.

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.

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.

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.

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 MCP hosts to run provenance-aware computational epitope research workflows, including sequence and immune-evidence analysis, structure and chemistry calculations, molecular docking, and checksummed 3D artifact exports.

Enables users to search multiple public life-science data repositories (GEO, ENA, CELLxGENE, PRIDE, DataCite) with a single query, returning a unified ranked list of datasets with ontology-expanded terms and per-source error reporting.

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

Enables AI assistants to search, browse, and retrieve interactive cell images and subcellular location data, including cell types, SVG illustrations, and location details through natural-language tool calls.

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 assistants to query the eggNOG 7 database in natural language for protein lookups, orthologous groups, pairwise orthologs, protein families, taxonomy, and database statistics. Also delivers structured functional annotations such as KEGG KO and GO terms with confidence scores, plus an index of bulk-downloadable data files.

Enables LLM-powered applications to look up bacterial and archaeal taxonomy, search genomes, browse and navigate the taxonomic tree, and compare genomes or find phylogenetic paths between taxa. It works out of the box with a built-in reference dataset covering major phyla and can be pointed at full Genome Taxonomy Database TSV files for comprehensive queries.

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.