Examples scripts

SemMedDB Knowledge Graph

1. Get all genomic entities that interacts with one or more genomic entities

python examples/scripts/read_from_neo4j.py --host localhost --bolt_port 7687 \
    --username <username> \
    --password <password> \
    --filter subject_category=genomic_entity \
    --filter edge_label=interacts_with \
    --filter object_category=genomic_entity

• Total number of nodes loaded: 20656
• Total number of edges loaded: 171811

2. Get all chemical substances and what diseases they treat

python examples/scripts/read_from_neo4j.py --host localhost --bolt_port 7687 \
    --username <username> \
    --password <password> \
    --filter subject_category=chemical_substance \
    --filter edge_label=treats \
    --filter object_category=disease

• Total number of nodes loaded: 49713
• Total number of edges loaded: 516334

3. Get all chemical substances and the biological process that they affect

python examples/scripts/read_from_neo4j.py --host localhost --bolt_port 7687 \
    --username <username> \
    --password <password> \
    --filter subject_category=chemical_substance \
    --filter edge_label=affects \
    --filter object_category=biological_process

• Total number of nodes loaded: 43587
• Total number of edges loaded: 658355

4. Get all anatomical entities and the disease that they are associated with

python examples/scripts/read_from_neo4j.py --host localhost --bolt_port 7687 \
    --username <username> \
    --password <password> \
    --filter subject_category=anatomical_entity \
    --filter edge_label=location_of \
    --filter object_category=disease

• Total number of nodes loaded: 36179
• Total number of edges loaded: 510709

5. Get all activities and behaviors and the diseases that they predispose to

python examples/scripts/read_from_neo4j.py --host localhost --bolt_port 7687 \
    --username <username> \
    --password <password> \
    --filter subject_category=activity_and_behavior \
    --filter edge_label=predisposes \
    --filter object_category=disease

• Total number of nodes loaded: 1960
• Total number of edges loaded: 5493

6. Get all chemical substances and the diseases that they cause

python examples/scripts/read_from_neo4j.py --host localhost --bolt_port 7687 \
    --username neo4j \
    --password <password> \
    --filter subject_category=chemical_substance \
    --filter edge_label=causes \
    --filter object_category=disease

• Total number of nodes loaded: 37977
• Total number of edges loaded: 299806