"How to write a query in Elasticsearch" 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.

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.

Enables researchers to query public ENA and BioSamples genomics data in plain English through any MCP client, including counting records, searching samples, retrieving sample details, and checking metadata quality against project requirements.

Provides seamless access to the Protein Data Bank in Europe (PDBe) API and search capabilities, enabling AI clients to query protein structures, perform advanced searches, and retrieve structural biology data.

Search PubMed for articles matching the query.

Enables AI assistants to query VirtualFlyBrain data, run queries, and search for terms related to Drosophila neurobiology.

Enables AI agents to query clinical genomics databases, retrieve supporting literature, analyze population genetics, and visualize biological pathways.

Provides tools to query and resolve identifiers from the Bioregistry, including prefix metadata, CURIE resolution, and substring search.

Enables AI agents to query Protein Data Bank in Europe (EBI) structural data by 4-character PDB ID, retrieving entry summaries, molecule/entity listings with chain lengths, and SIFTS cross-database mappings to UniProt accessions and residue ranges. Runs as a hosted gateway endpoint or a local stdio server with no authentication required.

A local-first MCP server that annotates whole-genome VCF files and lets you query pharmacogenomics, disease risk, and carrier status through natural language.

Enables AI agents to query the WikiPathways open community pathway database via natural language, part of the Pipeworx MCP gateway.

Enables AI assistants to query VCF files through MCP tools that summarize variants, identify pathogenic and carrier variants, interpret pharmacogenomic results, and determine APOE status, with web app and Claude Desktop support.

Control PyMOL from Cursor via natural language. Enables describing molecular structures and styles in plain language to execute PyMOL commands through XML-RPC.

Enables LLMs and AI agents to query a biomedical knowledge graph stored in RedisGraph, with tools for concept search, synonym enrichment, and study variable discovery through semantic relationships.

An MCP server that grounds protein research in the UniProt SPARQL endpoint, providing tools for querying proteins, sequences, variants, diseases, and more via intent-named tools and raw SPARQL.

Enables language models to search biomedical literature, fetch sequences, and follow links across Entrez databases through eleven read-only tools wrapping the nine NCBI Entrez E-utilities. It handles URL building, pacing, redirects, response caps, and API-key redaction so queries can be answered without a browser or scraping.

Grounds gene-nomenclature work in the HUGO Gene Nomenclature Committee (HGNC) dataset, enabling resolution of gene symbols and IDs to canonical HGNC identifiers, plus cross-references and batch operations.

Enables AI assistants to clean PDB structures and run initial-stage energy relaxation for biomolecular modeling. It provides a structured workflow for preparing structures before production molecular dynamics or coarse-graining pipelines.

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.