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Neo4j Database format

hetionet-v1.0.db.tar.bz2 is a bzip2-compressed tarball of a Neo4j database. The database has been migrated to the Neo4j 3.0.1 Community Edition.


The Neo4j graph uses slightly different names for metanodes (Neo4j labels) and metaedges (Neo4j relationship types). See labels.tsv for the node type mapping and types.tsv for the edge type mapping. We conform to the Neo4j style of CamelCase labels and ALL_CAPS relationship types. In addition, Neo4j relationship types are appended with metaedge standard abbreviations. This adds source/target metanode awareness to relationship types and enables optimized queries.

Neo4j setup instructions

Download and extract Neo4j 3.0 Community Edition from Neo4j. Make sure the Neo4j server is stopped. Navigate to the data/databases directory inside the Neo4j directory and run:

# Backup graph.db directory if it exists
if [ -d "graph.db" ]; then
  mv graph.db graph.db.backup_`date +%F`

# Download and extract graph.db for Hetionet v1.0
curl --location | tar --extract --bzip2

If curl throws an error related to SSL or certificates, you can add the --insecure argument to curl to allow connections to SSL sites without certs.

The above commands should create a graph.db directory inside data. You should now be able to power up your Neo4j server. Once the server is running you can access the browser at http://localhost:7474/. Delete the graph.db directory to uninstall Hetionet as the default Neo4j database.

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