A
licenseA
qualityA
maintenanceA 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.
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"Exploring the term 'Make' or related resources" matching MCP servers:
- AlicenseAqualityAmaintenanceMCP 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.17MIT
- AlicenseAqualityDmaintenanceEnables AI assistants to query the Ubergraph biomedical ontology SPARQL endpoint with tools for custom SPARQL queries, term lookup, search, and hierarchy traversal.4MIT
- FlicenseBqualityDmaintenanceA production-ready Model Context Protocol (MCP) server that provides comprehensive access to the BioOntology API for searching, annotating, and exploring over 1,200 biological ontologies.109
- FlicenseBqualityDmaintenanceA comprehensive Model Context Protocol (MCP) server that provides access to the AlphaFold Protein Structure Database through a rich set of tools and resources for protein structure prediction analysis.1935
- FlicenseBqualityDmaintenanceA 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.218
- AlicenseNot gradedqualityDmaintenanceEnables molecular generation, optimization, and analysis through NVIDIA MolMIM API. Supports generating drug-like molecules with desired properties, extracting molecular embeddings, and exploring chemical space around seed molecules.MIT
- AlicenseNot gradedqualityCmaintenanceEnables querying and browsing ontologies from the EBI Ontology Lookup Service, including searching for terms, retrieving term details, and navigating ontology hierarchies via natural language.8MIT
- AlicenseNot gradedqualityCmaintenanceEnables querying of the Monarch Initiative biomedical knowledge graph for genes, diseases, phenotypes, and their associations through natural language or direct tool calls.10MIT
- AlicenseNot gradedqualityAmaintenanceFederates 13 gene-related MCP backends (gnomAD, GTEx, etc.) behind a single Streamable HTTP endpoint with collision-free namespacing and search-based tool discovery.2MIT
- AlicenseNot gradedqualityCmaintenanceEnables querying the Human Protein Atlas data using natural language or direct MCP tools, with keyless access via the Pipeworx gateway.5MIT
- AlicenseNot gradedqualityFmaintenanceEnables AI assistants to query VirtualFlyBrain data, run queries, and search for terms related to Drosophila neurobiology.MIT
- AlicenseNot gradedqualityFmaintenanceExecutes SPARQL queries against biological and biomedical RDF databases from the RDF Portal, with additional REST API integrations for bioinformatics resources.1MIT
- FlicenseNot gradedqualityDmaintenanceEnables 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.1
- FlicenseNot gradedqualityDmaintenanceEnables search and retrieval of academic papers from PubMed database with advanced features like MeSH term lookup, publication statistics, and PICO-based evidence search.5
- FlicenseAqualityDmaintenanceEnables 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.9
- AlicenseAqualityCmaintenanceEnables coding agents to interact with the Reactome pathway database, including search, lookup, hierarchy traversal, SBML/SBGN export, and gene-set enrichment analysis.17MIT
- AlicenseAqualityCmaintenanceProvides direct SQL access to a locally hosted Reactome database, enabling schema discovery, guarded read-only queries, and ergonomic helpers over the full relational schema.9MIT
- AlicenseAqualityDmaintenanceRenders interactive 2D molecular structure diagrams from SMILES notation and computes molecular properties like molecular weight, LogP, and TPSA, directly in the chat.1601ISC
CEDAR MCP Serverofficial
AlicenseAqualityAmaintenanceEnables interaction with the CEDAR metadata repository, including fetching templates, searching BioPortal ontology terms, and managing template instances.8MIT