everycure-kg

Everycure Knowledge Graph Skill

Overview

The Everycure KG is a massive biomedical knowledge graph (9.2M nodes, 77M relationships) built on the Biolink Model. It integrates data on drugs, diseases, genes, proteins, pathways, and their relationships.

Key Challenge: The graph is extremely densely connected. Naive queries cause path explosion (~440x growth per hop).

Safety Built-In: The MCP server includes automatic safety checks:

• Warns on high-degree nodes (>1K edges)
• Blocks queries on super-hubs (>10K edges)
• Prevents path explosion before executing queries
• Handles schema quirks automatically in predefined metapaths

This skill teaches you to query effectively and work within the safety guardrails.

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Quick Start

Finding Drug Repurposing Opportunities

Question: "Does Metformin treat Idiopathic Pulmonary Fibrosis?"

Step 1: Find node IDs

# Use execute_cypher to find nodes
result = execute_cypher("""
    MATCH (d) WHERE d.name CONTAINS 'Metformin' AND 'biolink:Drug' IN labels(d)
    RETURN d.id, d.name LIMIT 5
""")
# Result: CHEBI:6801

result = execute_cypher("""
    MATCH (dis) WHERE dis.name CONTAINS 'pulmonary fibrosis' AND 'biolink:Disease' IN labels(dis)
    RETURN dis.id, dis.name LIMIT 5
""")
# Result: MONDO:0800029

Step 2: Check direct treatment relationship (1-hop)

result = find_paths_by_metapath(
    source_id="CHEBI:6801",
    target_id="MONDO:0800029",
    metapath_name="drug_to_disease_direct"
)
# Result: FOUND - Direct treatment relationship exists!

Step 3: Find mechanistic targets (2-hop)

result = find_paths_by_metapath(
    source_id="CHEBI:6801",
    target_id="MONDO:0800029",
    metapath_name="drug_to_disease_via_target"
)
# Result: 50+ proteins including HDAC6 (AMPK pathway)

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Core Principles

1. Always COUNT Before RETURN

Path explosion happens when you RETURN data before counting.

// WRONG (will hang on large results):
MATCH (d)-[r1]-(mid)-[r2]-(target)
WHERE d.id = $drug_id
RETURN d, mid, target LIMIT 100

// CORRECT (count first):
MATCH (d)-[r1]-(mid)-[r2]-(target)
WHERE d.id = $drug_id
RETURN COUNT(*) as path_count
// If path_count < 1000, then run:
// MATCH... RETURN d, mid, target LIMIT 100