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  • A
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    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.
    11
    MIT
  • A
    license
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    quality
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    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.
    17
    1
    MIT
  • A
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    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.
    5
    Apache 2.0
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    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.
    10
    434 npm
    9
    Apache 2.0
  • A
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    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.
    11
    5,958 npm
    148
    Apache 2.0
  • A
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    quality
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    Enables AI assistants to query the Ubergraph biomedical ontology SPARQL endpoint with tools for custom SPARQL queries, term lookup, search, and hierarchy traversal.
    4
    MIT
  • F
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    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.
    23
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  • F
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    A Model Context Protocol (MCP) server that provides access to the Protein Data Bank (PDB) - the worldwide repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.
    5
    26
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    quality
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    Enables LLM agents to query the CZ CELLxGENE Census single-cell atlas with ontology-aware filters, cost caps, and full provenance, allowing natural language questions about cell types, tissues, and gene expression.
    13
    20 PyPI
    MIT
  • F
    license
    B
    quality
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    A Model Context Protocol server that enhances language models with protein structure analysis capabilities, enabling detailed active site analysis and disease-related protein searches through established protein databases.
    2
    18
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  • A
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    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.
    1 npm
    MIT
  • A
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    Enables querying of the Monarch Initiative biomedical knowledge graph for genes, diseases, phenotypes, and their associations through natural language or direct tool calls.
    2 npm
    MIT
  • A
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    maintenance
    Federates 13 gene-related MCP backends (gnomAD, GTEx, etc.) behind a single Streamable HTTP endpoint with collision-free namespacing and search-based tool discovery.
    6
    MIT
  • A
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    Enables AI assistants to query VirtualFlyBrain data, run queries, and search for terms related to Drosophila neurobiology.
    MIT
  • A
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    quality
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    Enables querying metadata from MyVariant.info, a comprehensive variant annotation database, providing dataset statistics, source information, and build versions.
    1 npm
    MIT
  • A
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    Resolves free-text condition and disease strings — trial-registry condition fields, drug-label indications, hand-typed wording — onto the Mondo Disease Ontology, returning the best term id and label along with a trustworthy match-quality label (exact label/synonym, broader, narrower, fuzzy, or no-match) plus cross-ontology xrefs. Optionally expands a resolved term to all of its descendant ids for building subtype-inclusive registry filters.
    52 npm
    MIT