See Reactome's official documentation regarding downloading the Reactome Knowledgebase.
See below for unofficial user hints ...
- Download the Reactome database
- Uncompress and extract the database
- Ensure the graph.db directory does not exist in the Neo4j directory structure
- Moved the Reactome database to the Neo4j graph.db directory
- Start the neo4j server on the new Reactome Knowledgebase
- View the Reactome database in the neo4j browser
- Python interface to neo4j:
7.1) Install the Python package, neo4j
7.2) Connect to the neo4j server from a Python script
Download from https://reactome.org/dev/graph-database or
wget https://reactome.org/download/current/reactome.graphdb.tgz
$ tar -xzvf reactome.graphdb.tgz
reactome.graphdb.v67/
reactome.graphdb.v67/neostore.labeltokenstore.db.names.id
reactome.graphdb.v67/neostore.nodestore.db.id
reactome.graphdb.v67/neostore.propertystore.db.index.id
reactome.graphdb.v67/neostore.relationshipstore.db.id
reactome.graphdb.v67/neostore.counts.db.a
reactome.graphdb.v67/neostore.propertystore.db.strings
...
Does the graph.db directory exist?
No? Go to step 4.
$ cd ~/neo4j/neo4j-community-4.1.9/data/databases/
$ ls graph.db
ls: cannot access 'graph.db': No such file or directory
Yes? Move it out of the way:
$ ls graph.db
debug.log neostore.nodestore.db.labels neostore.relationshipgroupstore.db.id
index neostore.nodestore.db.labels.id neostore.relationshipstore.db
neostore neostore.propertystore.db neostore.relationshipstore.db.id
...
$ mv graph.db graph.db.v66
$ ls graph.db
ls: cannot access 'graph.db': No such file or directory
$ mv reactome.graphdb.v67 ~/neo4j/neo4j-community-4.1.9/data/databases/graph.db
# Confirm it is moved
$ cd ~/neo4j/neo4j-community-4.1.9/data/databases/graph.db
$ ls graph.db
debug.log neostore.nodestore.db.labels neostore.relationshipgroupstore.db.id
index neostore.nodestore.db.labels.id neostore.relationshipstore.db
neostore neostore.propertystore.db neostore.relationshipstore.db.id
...
Where to look if it does not work
$ neo4j/neo4j-community-4.1.9/bin/neo4j start
Active database: graph.db
Directories in use:
home: /home/neo4j/neo4j/neo4j-community-4.1.9
config: /home/neo4j/neo4j/neo4j-community-4.1.9/conf/
logs: /home/neo4j/neo4j/neo4j-community-4.1.9/logs
plugins: /home/neo4j/neo4j/neo4j-community-4.1.9/plugins
import: /home/neo4j/neo4j/neo4j-community-4.1.9/import
data: /home/neo4j/neo4j/neo4j-community-4.1.9/data
certificates: /home/neo4j/neo4j/neo4j-community-4.1.9/certificates
run: /home/neo4j/neo4j/neo4j-community-4.1.9/run
Starting Neo4j.
WARNING: Max 1024 open files allowed, minimum of 40000 recommended. See the Neo4j manual.
Started neo4j (pid 545). It is available at http://localhost:7474/
There may be a short delay until the server is ready.
See /home/neo4j/neo4j/neo4j-community-4.1.9/logs/neo4j.log for current status.
Look at the bottom of both the debug.log and the neo4j.log
$ find neo4j-community-4.1.9/logs -type f
neo4j-community-4.1.9/logs/debug.log
neo4j-community-4.1.9/logs/neo4j.log
The neo4j config file is at /home/neo4j/neo4j/neo4j-community-4.1.9/conf/neo4j.conf
if seen in the debug.log
file:
Neo4j cannot be started because the database files require
upgrading and upgrades are disabled in the configuration.
Please set 'dbms.allow_upgrade' to 'true' in your
configuration file and try again.
Setting both Username and Password to neo4j worked for us when loading a new Reactome database version for the first time.
To change your password again:
:server change-password
In your browser, go to: http://localhost:7474/browser/
Click on the Database icon at the upper left corner (which should be green after clicking on it); there should be lots of Node Labels:
What sub-pathways are under under pathway, R-HSA-983169, Class I MHC mediated antigen processing & presentation?
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