A
license-
qualityC
maintenanceEnables querying of the Monarch Initiative biomedical knowledge graph for genes, diseases, phenotypes, and their associations through natural language or direct tool calls.
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MIT
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"Definition and meaning of the word 'word'" matching MCP servers:
- Alicense-qualityDmaintenanceEnables interaction with AnnData objects via the Model Context Protocol, allowing querying and manipulation of annotated data matrices for single-cell genomics.2MIT
- Alicense-qualityDmaintenanceValidates the physical and chemical plausibility of ligand–protein docking poses using the PoseBusters tool.5BSD 3-Clause
- Alicense-qualityCmaintenanceEnables AI agents to query the WikiPathways open community pathway database via natural language, part of the Pipeworx MCP gateway.3MIT
- Alicense-qualityCmaintenanceEnables querying the EBI Expression Atlas for gene expression data across species and conditions. Part of the Pipeworx gateway, it provides access to baseline and differential expression studies.7MIT
- Flicense-qualityCmaintenanceEnables querying the CIViC database for clinical interpretations of cancer variants through tools like get_variant_evidence and get_variant_assertions.1
- AlicenseAqualityAmaintenanceGrounds 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.9MIT
- AlicenseAqualityAmaintenanceEnables 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.11MIT
- AlicenseAqualityDmaintenanceRenders interactive 2D molecular structure diagrams from SMILES notation and computes molecular properties like molecular weight, LogP, and TPSA, directly in the chat.1601ISC
- FlicenseAqualityCmaintenanceEnables analysis of bulk RNA-seq data using natural language queries, executing R and Python in a Docker container with automatic sample anonymization and privacy controls.7
- AlicenseAqualityBmaintenanceMCP server that exposes the UniProt REST API to LLM clients, enabling search and retrieval of protein data via tools like search_uniprotkb, get_entry, and map_ids.7MIT
io.github.rcsb/rcsb-mcpofficial
AlicenseAqualityBmaintenanceEnables discovery, inspection, and cross-referencing of Protein Data Bank structures through three RCSB APIs: search, data, and sequence coordinates.363MIT
Noctua MCP Serverofficial
AlicenseAqualityCmaintenanceEnables 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.18BSD 3-Clause- AlicenseAqualityBmaintenanceConverts natural language queries into Cypher queries against the NASA GeneLab Knowledge Graph, enabling AI-assisted analysis of spaceflight experiments and their biological effects.123BSD 3-Clause
- AlicenseAqualityDmaintenanceAn MCP server that provides tools for searching and fetching protein data from the UniProt database using the unipressed library.2MIT
- AlicenseAqualityAmaintenanceAn MCP server for querying the KEGG bioinformatics database, providing tools, resource templates, and guided prompts for pathways, genes, compounds, and more.343MIT
- AlicenseAqualityCmaintenanceMCP server for single-cell lineage tracing analysis, enabling conversational reconstruction, visualization, and heritability analysis of lineage trees using Cassiopeia, pycea, and treedata.18MIT
- AlicenseAqualityDmaintenanceEnables AI assistants to query the Ubergraph biomedical ontology SPARQL endpoint with tools for custom SPARQL queries, term lookup, search, and hierarchy traversal.4MIT
- AlicenseAqualityCmaintenanceConnects 3D Slicer with AI assistants through the Model Context Protocol, enabling medical image processing and scene manipulation using natural language.338MIT
- AlicenseAqualityAmaintenanceProvides LLMs with structured access to critical biomedical databases including PubTator3 (PubMed/PMC), ClinicalTrials.gov, and MyVariant.info through the Model Context Protocol.35596MIT