Unsuccesful loading of Reactome database to Neo4j

Question

I'm trying to load Reactome database into my Neo4j Desktop.

I downloaded the latest version of the database from Reactome website (https://reactome.org/dev/graph-database#GetStarted), version of my Neo4j Desktop is 1.3.4 and for the created database I'm using Neo4j 4.1.1 (tried 4.1.0 as well).

Afterwards, I extracted the tar.gz file and used the terminal in Neo4j Desktop to restore the data in my database with the following command:

bin/neo4j-admin restore --from=/PATH/reactome.graphdb/graph.db --database=graph.db

And pressed Start button. Start was successful, so I opened it in Neo4J Browser - here it came with notification:

Database 'neo4j' is unavailable. Run :sysinfo for more info.

I checked the debug.log: the problem should be in disabled upgrade option in neo4j.conf file debug.log - screenshot

So I uncommented the option to: dbms.allow_upgrade=true

But when I tried to run the dataset with Start button I got only the notification:

Database failed to start: DB [database-e25f8ba8-dea1-4e70-8944-024f73a2eeaf] 'v4.1.1' exited with status 'KILLED'. Check the logs

After checking the logs I found this: neo4j.log - printscreen

I'm truly stacked now. Does anyone have any idea how to deal with this issue? Thanks a lot!

Answer 1

You may want to use the following script with reactome.graphdb.dump file:

bin/neo4j-admin load --from=/PATH/reactome.graphdb.dump --database=reactome --force