Previously I had a problem when making a \'backup\' as shown in this question where I get an error when trying to restore the database because I did a copy when the database
Online backup, in a sense of taking a consistent backup while Neo4j is running, is only available in Neo4j enterprise edition. Enterprise edition's backup also features a verbose consistency check of the backup, something you do not get in community either.
The only safe option in community edition is to shutdown Neo4j cleanly and copy away the graph.db folder recursively. I'm typically using:
cd data
tar -zcf graph.db.tar.gz graph.db/
For restoring you shut down neo4j, clean out a existing graph.db folder and restore the original graph.db folder from your backup:
cd data
rm -rf graph.db
tar -zxf graph.db.tar.gz