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Last active December 22, 2023 15:59
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HOWTO: Use neo4j V5 with reactome database
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howto-neo4j5-reactome.md

Reactome dumps are in Neo4j 4 format. To use them with Neo4j 5 the Reactome database needs to be downloaded as a dump and converted:

  • Following instructions are for CLI installation of Neo4j (Linux)
  • Install any 5.* version of Neo4j (tested with neo4j-community-5.15.0)
  • Download Reactome database dump from https://reactome.org/download/current/reactome.graphdb.dump
  • cd to installation directory, all commands below from there
  • cp <PATH OF DOWNLOADED DUMP> reactome.dump (so the dump file is in the same directory, also the file is renamed because dots in the database name are not allowed)
  • ./bin/neo4j-admin database migrate --force-btree-indexes-to-range reactome
  • Now there should be a new directory created under data/databases
  • Don't forget to add these lines in conf/neo4j.conf:
initial.dbms.default_database=reactome
db.recovery.fail_on_missing_files=false
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