"Setting up SQL Server connections for agent querying" matching MCP servers:

Enables compiling typed decision queries into the smallest decision-sufficient evidence context with machine-checkable Context Certificates, providing auditable executable-biology inference through local MCP tools.

Enables AI agents to read and manipulate networks, tables, visual styles, and more in a live Cytoscape Web session through natural language, by connecting over Chrome DevTools Protocol.

Enables prediction of blood-brain barrier permeability for drug molecules via machine learning, with molecule name lookup, plain-language explanations, similar drug search, and applicability domain checks. Exposes these as MCP tools and orchestrates them via a LangGraph agent.

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.

An MCP server for querying the KEGG bioinformatics database, providing tools, resource templates, and guided prompts for pathways, genes, compounds, and more.

Enables querying and accessing hivtools data through a REST API and MCP-compatible tools.

Agent-callable canine genomics API providing breed-stratified allele frequencies, pathogenicity predictions, and variant-gene-breed-disease knowledge graph for dog DNA.

Enables querying gene expression experiments, brain region structure ontologies, and in-situ hybridization datasets from the Allen Institute's Brain Atlas public API.

Enables querying the gnomAD genome aggregation database for variant, gene, and region information.

Enables querying and browsing ontologies from the EBI Ontology Lookup Service, including searching for terms, retrieving term details, and navigating ontology hierarchies via natural language.

MCP server for querying gene annotations, full-text gene search, and species taxonomy via MyGene.info. Enables AI agents to access gene data through natural language questions.

Enables querying of the Monarch Initiative biomedical knowledge graph for genes, diseases, phenotypes, and their associations through natural language or direct tool calls.

Enables querying dbSNP refSNP records and converting between HGVS, SPDI, and rsID identifiers for human genetic variants, with assembly-aware genomic placement and population frequencies.

Enables querying roughly 3.2 million measured protein–ligand binding affinities from a local, read-only DuckDB build of the BindingDB MySQL dump, with tools for searching compounds and targets, retrieving potency and selectivity profiles, fetching activity records with assay and citation details, and running read-only SQL.

Enables querying HERB 2.0's Traditional Chinese Medicine knowledge base for herbs, ingredients, gene targets, diseases, PubMed-cited papers, and GEO transcriptomic experiments, with each relationship tagged by evidence tier.

MCP server for querying BV-BRC biological data, submitting analysis jobs (assembly, annotation, BLAST, etc.), and managing workspace files via natural language.

MCP server that enables querying GlyGen for summaries of proteins, glycans, sites, biomarkers, and diseases.

Enables interaction with AnnData objects via the Model Context Protocol, allowing querying and manipulation of annotated data matrices for single-cell genomics.

MCP server for STRING-DB that enables querying protein-protein interaction networks, functional enrichment, and homology mappings.

Enables users to look up yeast genes/loci, search genes and alleles by free text, and retrieve Gene Ontology annotations from the Saccharomyces Genome Database.

Enables looking up genes, fetching sequences, predicting variant consequences, finding orthologs, and cross-database xrefs via Ensembl REST API through MCP.

Enables querying GTEx gene expression, eQTL, and tissue data through an MCP gateway.

Look up variant allele frequencies by ancestry, gene loss-of-function constraint, gene variant lists, and sequencing coverage over gnomAD — with ClinVar significance joined in — via MCP.

Enables querying the BOLD Systems global DNA barcode database for specimen records, taxonomy, barcode sequences, and BIN clusters, with keyless access and FASTA-ready output.

Enables querying BindingDB for measured protein/small-molecule binding affinities, including finding ligands that bind a protein, protein targets for a compound, and affinities from PDB structures.

Enables MCP-compatible AI assistants to look up clinical variants and batch-annotate NGS spreadsheet outputs via ClinVar, gnomAD, and VarSome. Provides tools for variant lookup, Excel inspection, and folder-level batch processing.

Supports querying and downloading MGnify genome data and performing KEGG functional annotation and module completeness analysis for microbial genomes.

Enables querying the EBI Expression Atlas for gene expression data across species and conditions. Part of the Pipeworx gateway, it provides access to baseline and differential expression studies.

Enables querying ClinGen curated evidence for gene-disease validity, dosage, actionability, and variant pathogenicity via MCP tools.

MCP server for querying the EBI PRIDE Archive, a proteomics (mass-spectrometry) data repository, through natural language or direct tool calls.