"A tool for querying web pages saved in browser bookmarks" matching MCP servers:

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

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

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.

Provides comprehensive access to the UCSC Genome Browser API, enabling queries of genomic data, DNA sequences, gene annotations, variants, and metadata across multiple species and assemblies.

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 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.

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.

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

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

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

Enables AI assistants to search and retrieve prokaryotic names, taxon details, full classifications, and rank-based browsing from the List of Prokaryotic names with Standing in Nomenclature in real time, plus read related information pages.

Enables querying of per-residue missense tolerance, Pfam domain annotations, and variant counts for human transcripts by wrapping the MetaDome web service. Provides MCP tools for resolving transcripts, requesting tolerance landscapes, and identifying constrained regions.

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.

MCP server for querying the GWAS Catalog (EBI/NHGRI), a curated catalog of genome-wide association studies. It enables AI agents to search and retrieve study data via natural language or direct tool calls.

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.

Enables querying the SymMap v2 Traditional Chinese Medicine association graph, covering herbs, ingredients, protein targets, symptoms, syndromes, and diseases with evidence-tiered relationships. It also supports plain-English questions through Pipeworx's ask_pipeworx meta-tool.

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.

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.

This server provides access to InterPro protein family, domain, and functional-site classification data from EBI. It allows querying protein annotations through natural language or direct tool calls.

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 querying Ensembl genomic data including gene lookup, sequence retrieval, homology, variation, and variant effect prediction via MCP tools.