PDBe Graph Database

This page provides information on how to setup the knowledge graph as a local Neo4J instance.

Documentation

Interactive documentation of the data available in the PDBe graph database is available here. To learn more about how to write Cypher queries to extract data from PDBe graph database, please visit PDBe graph queries.

Requirements

• Neo4J Community/Enterprise Edition 3.5 or Neo4J Community/Enterprise Edition 5(Download )
• There are two database files available on our FTP area: (https://ftp.ebi.ac.uk/pub/databases/msd/graphdb/):
  • graph.db.tgz → For Neo4J 3.5
  • neo4j.dump → For Neo4J 4 and above

Steps

For Neo4J 3.5 (Using graph.db.tgz)

• Download the graph.db.tgz archive
• Ensure the Neo4J instance is stopped
• Extract the database files:

  tar -xvzf graph.db.tgz -C $NEO4J_HOME/data/databases/

• Start Neo4J instance

For Neo4J 5 (Using neo4j.dump)

• Download the neo4j.dump file
• Ensure Neo4J instance is stopped
• Move the dump file to a suitable location, e.g.,

  mv neo4j.dump $NEO4J_HOME/data/dumps/

• Restore the database from the dump

  neo4j-admin database load neo4j --from-path=$NEO4J_HOME/data/dumps/

• Start Neo4J instance

PDBe Graph data will be available in the running instance. Start exploring!