nexotype-mcp 0.4.2

Nexotype MCP Server — biomedical knowledge graph for drug discovery, genomics, and market intelligence

Nexotype MCP Server

AI-powered biomedical knowledge graph for drug discovery, genomics, and market intelligence.

Connect your AI tools to the Nexotype platform and query the biomedical knowledge graph through conversation.

Installation

pip install nexotype-mcp

Or with uv:

# Install uv (if not already installed)
brew install uv

# Add uv tools to PATH (one-time setup)
echo 'export PATH="$HOME/.local/bin:$PATH"' >> ~/.zshrc
source ~/.zshrc

# Install nexotype-mcp
uv tool install nexotype-mcp

Already installed? Update:

pip install --upgrade nexotype-mcp
# or
uv tool upgrade nexotype-mcp

Authentication

nexotype-cli login

Enter your email and password. Credentials are stored securely at ~/.nexotype/credentials.json (chmod 600).

Configure Your AI Client

Claude Desktop

Edit ~/Library/Application Support/Claude/claude_desktop_config.json (macOS) or %APPDATA%\Claude\claude_desktop_config.json (Windows):

{
  "mcpServers": {
    "nexotype": {
      "command": "nexotype-mcp"
    }
  }
}

Claude Code

claude mcp add nexotype -- nexotype-mcp

VS Code / Cursor

Add to your MCP settings:

{
  "nexotype": {
    "command": "nexotype-mcp"
  }
}

Restart the application after saving.

Tools (28)

Graph Intelligence (6 tools)

Tool	Description
explore_network	N-hop neighborhood of any entity
find_path	Shortest path between two entities
find_similar	Entities sharing the most relationships
company_deep_dive	Full portfolio of a pharma/biotech company
drug_discovery	Targets, pathways, indications for a drug
competitive_landscape	All drugs and companies targeting a protein

AI Query (1 tool)

Tool	Description
ask_knowledge_graph	Natural language question → grounded answer from graph

Search & Browse (2 tools)

Tool	Description
search_entities	List entities of any of the 61 types
get_entity	Full details for a specific entity

Context (3 tools)

Tool	Description
get_permissions	Check subscription tier and domain access
list_subjects	List available biological subjects
set_subject	Set active subject for personalization tools

Personalized Health (10 tools)

Tool	Description
get_user_profile	Personal info linked to the subject
list_user_variants	Detected genomic variants
list_biomarker_readings	Time-series health data
create_biomarker_reading	Log a new biomarker measurement
list_treatment_logs	Intervention history
create_treatment_log	Log a new treatment
list_pathway_scores	Pathway health scores
list_recommendations	Personalized treatment suggestions
upload_genomic_file	Upload VCF/23andMe file for analysis
get_processing_status	Check genomic file processing progress

Commercial Intelligence (6 tools)

Tool	Description
list_market_organizations	Pharma/biotech companies
get_market_organization	Full company details
list_patents	Patent filings and status
list_development_pipelines	Clinical trial phases
list_regulatory_approvals	FDA/EMA approvals
list_licensing_agreements	Commercial partnerships

Example Queries

"What drugs target EGFR and are in Phase III?"
"Show me Novo Nordisk's full portfolio"
"What variants are associated with Alzheimer's risk?"
"Compare GLP-1 receptor agonists across companies"
"Who else is targeting mTOR?"
"List all therapeutic peptides in the database"
"What are my detected genomic variants?"

CLI Commands

Command	Description
nexotype-cli login	Authenticate via browser (OAuth device flow)
nexotype-cli login --basic	Authenticate with email/password (headless fallback)
nexotype-cli logout	Delete stored credentials
nexotype-cli status	Show current auth status

Environment Variables

Variable	Default	Description
NEXOTYPE_API_URL	http://localhost:8000	API server URL