"Understanding Integrated Knowledge Graphs" matching MCP servers:

• paperSearch

  FreddieWho

  A

  license

  -

  quality

  A

  maintenance

  Enables AI coding agents to search academic papers, resolve biomedical entities, mine relations, and traverse citation graphs using Semantic Scholar and PubTator3, with local caching for reproducibility.

  Last updated 2026-07-10

  MIT

• OrigeneMCP

  GENTEL-lab

  F

  license

  -

  quality

  D

  maintenance

  An advanced integrated MCP server platform that combines 600+ tools and multiple biomedical databases to enable comprehensive information retrieval across molecules, proteins, genes, and diseases for accelerating therapeutic research.

  Last updated 2026-02-24

  37
• 

  Noctua MCP Serverofficial

  geneontology

  A

  license

  A

  quality

  C

  maintenance

  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.

  Last updated 2025-11-01

  18

  BSD 3-Clause

• MCP GeneLab Server

  sbl-sdsc

  A

  license

  A

  quality

  B

  maintenance

  Converts natural language queries into Cypher queries against the NASA GeneLab Knowledge Graph, enabling AI-assisted analysis of spaceflight experiments and their biological effects.

  Last updated 2026-07-21

  12

  3

  BSD 3-Clause
• 

  BioContextAI Knowledgebase MCPofficial

  biocontext-ai

  A

  license

  A

  quality

  C

  maintenance

  An MCP server that provides standardized access to biomedical knowledge bases and resources, enabling AI systems to retrieve verified information from sources like bioRxiv, EuropePMC, and various protein/gene databases.

  Last updated 2026-01-12

  52

  28

  Apache 2.0

• AlphaFold Sovereign MCP

  smaniches

  A

  license

  A

  quality

  B

  maintenance

  Integrates AlphaFold DB and eight other biomedical data sources into MCP tools for variant clinical reporting, disease-target analysis, structural intelligence, and drug repurposing, with results persisted to a local SQLite knowledge graph.

  Last updated 2026-07-29

  29

  4

  Apache 2.0

• SCMCP

  huang-sh

  A

  license

  C

  quality

  C

  maintenance

  An MCP server that enables single-cell RNA sequencing analysis through natural language, supporting data processing, visualization, and analysis tasks without requiring coding knowledge.

  Last updated 2025-05-15

  52

  12

  BSD 3-Clause
• 

  sniff-mcpofficial

  Sniffscore

  A

  license

  -

  quality

  B

  maintenance

  Agent-callable canine genomics API providing breed-stratified allele frequencies, pathogenicity predictions, and variant-gene-breed-disease knowledge graph for dog DNA.

  Last updated 2026-07-02

  MIT

• mcp-monarch-initiative

  pipeworx-io

  A

  license

  -

  quality

  C

  maintenance

  Enables querying of the Monarch Initiative biomedical knowledge graph for genes, diseases, phenotypes, and their associations through natural language or direct tool calls.

  Last updated 2026-06-02

  15

  MIT

• mcp-uniprot

  pipeworx-io

  A

  license

  -

  quality

  C

  maintenance

  Provides access to UniProt protein sequence and function knowledge base, enabling search and retrieval of protein entries, proteomes, taxonomy, and feature annotations.

  Last updated 2026-06-26

  3

  MIT

• Redis Graph MCP Server

  yskale

  F

  license

  -

  quality

  B

  maintenance

  Enables LLMs and AI agents to query a biomedical knowledge graph stored in RedisGraph, with tools for concept search, synonym enrichment, and study variable discovery through semantic relationships.

  Last updated 2026-05-19

• cellosaurus-mcp-server

  QuentinCody

  F

  license

  -

  quality

  B

  maintenance

  Enables querying and retrieving cell line records from the Cellosaurus knowledge base via its REST API, including searching, fetching by accession, and accessing release information.

  Last updated 2026-07-28