Node disappears after restart server. Neo4j 3.0 Cypher 3 - neo4j

Question

I'm trying to add a node to my base, but every time I restart the server, the node disappears along with their relationships.
I started my base by importing a CSV using the ./neo4j-import script in the bin folder. The node in question is a node that connects to all subgraphs of my base (like a root node), turning the base into a connected graph.
I already added through the shell (./neo4j-shell) through the web application and using python (using from neo4j.v1 driver import GraphDatabase), in all cases when I restart the server, the node disappears.
The command I am using in all approaches is this:
neo4j-sh (?)$ create(r:PDB{name: 'root', resolution: 'less than 2.0', method: 'x-ray diffraction'});
neo4j-sh (?)$ match(r:PDB{name:'root'}) match(p:PDB_FILE) merge(r)-[:HAS_PDB]->(p);
In the latest attempt used differently (using commit):
neo4j-sh (?)$ begin
neo4j-sh (?)$ create(r:PDB{name: 'root', resolution: 'less than 2.0', method: 'x-ray diffraction'});
neo4j-sh (?)$ match(r:PDB{name:'root'}) match(p:PDB_FILE) merge(r)-[:HAS_PDB]->(p);
neo4j-sh (?)$ commit
But without success.
I'm using version 3.0. * of Neo4j, Cypher 3.0, Ubuntu 4.14 server.

Answer 1

I have no idea on why this is happening to you, but what I would definitely try is using the super batch importer for huge datasets: neo4j-import. There is some instruction on how to use the tool in neo4j documentation.
To use the tool you have to put your data in special formats, individual csv files each corresponding to a type of node or a type of edge in your dataset. It is well explained in the given link, and, even though it does not explain why this is happening to you, it is surely worth a try.
Another things that you could try are:
to install neo4j in another machine. Maybe there is some weird problem with your installation/your system;
try another version of neo4j. I'm not totally aware, but I imagine the latter 2.X.X versions should be more stable than the newer ones, as Neo4j v3 has been release recently. It is easy to install any version using this debian repositories (via apt-get in Ubuntu).