"Querying Elasticsearch (ES)" matching MCP servers:

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

Enables natural language querying and analysis of KEGG biological databases, including pathways, genes, compounds, reactions, diseases, and drugs.

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 NCI Thesaurus and other cancer-research vocabularies served by NCI Enterprise Vocabulary Services, providing codes, synonyms, definitions, and hierarchical relationships via MCP tools.

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

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

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

Enables querying metadata from MyVariant.info, a comprehensive variant annotation database, providing dataset statistics, source information, and build versions.

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

Enables querying UCSC Genome Browser assemblies, annotation tracks, track data over genomic intervals, and raw DNA sequences across ~250 species without authentication.

Enables querying celltype markers from CellMarker database using natural language.

Enables querying the CIViC database for clinical interpretations of cancer variants through tools like get_variant_evidence and get_variant_assertions.

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.

An MCP server that enables AI coding assistants to interact with Rosetta, PyRosetta, and Biotite for running RosettaScripts, validating XML, translating between Rosetta and Biotite, scoring structures, and querying documentation.

Enables editing and querying of Gene Ontology Causal Activity Models (GO-CAMs) through the Barista API. Supports model creation, individual and fact management, evidence addition, and causal pathway construction for biological knowledge representation.

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.

Enables querying the EMBL-EBI catalog of published polygenic scores through read-only tools that search scores, traits, publications, performance metrics, sample sets, cohorts, and releases, and that trace GWAS studies and resolve ontology and ancestry identifiers. It also lists and downloads the associated scoring-file and metadata files from the catalog's FTP site.

Enables querying rare-variant, gene-based association results across ~1.2M individuals from 10 global biobanks, supporting phenome-wide scans, replication screens across ancestries, and candidate list evaluation for 44 harmonized traits.

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

Enables AI-driven pharmacogenomic analysis by querying structured genetic variant, drug response, and disease risk data. Supports natural language questions about medications, traits, and health risks based on user genome data, with privacy-first local execution.

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

Enables interaction with MGnify metagenomics resources and tools through the Model Context Protocol. Provides access to MGnify's API for querying and analyzing metagenomic datasets and related biological information.

A high-performance MCP server that gives LLMs access to 25 biomedical tools federated across 50+ upstream APIs for genes, variants, drugs, diseases, literature, clinical trials, and structural biology.

Enables querying genomics data from the Alliance of Genome Resources across model organisms including human, mouse, rat, zebrafish, fly, worm, yeast, and xenopus. Supports gene searches, disease associations, expression data, orthologs, phenotypes, and molecular interactions through natural language.

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.

Provides seamless access to UniProtKB protein data, enabling querying of protein entries, sequences, Gene Ontology annotations, and ID mappings through a typed, resilient interface.

Enables workflow management and Docker image building for Bio-OS platform. Supports WDL workflow submission, validation, and monitoring, along with Docker image building and status tracking for bioinformatics workflows.