README_download_hints.md

Reactome Download Hints

See Reactome's official documentation regarding downloading the Reactome Knowledgebase.

See below for unofficial user hints ...

Hints for downloading the Reactome Knowledgebase

1. Download the Reactome database
2. Uncompress and extract the database
3. Ensure the graph.db directory does not exist in the Neo4j directory structure
4. Moved the Reactome database to the Neo4j graph.db directory
5. Start the neo4j server on the new Reactome Knowledgebase
6. View the Reactome database in the neo4j browser
7. Python interface to neo4j:
   7.1) Install the Python package, neo4j
   7.2) Connect to the neo4j server from a Python script

Hints for downloading the Reactome Knowledgebase (details)

1. Download the Reactome database

Download from https://reactome.org/dev/graph-database or wget https://reactome.org/download/current/reactome.graphdb.tgz

2. Uncompress and extract the Reactome database in Neo4j format

$ 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
    ...

3. Ensure the graph.db directory does not exist in the Neo4j directory structure

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

4. Moved the Reactome database to the graph.db 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
    ...

5. Start the neo4j server on the new Reactome Knowledgebase

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.

Where to look if it does not work

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.

6. Connect to the server for the first time

Create a password

Setting both Username and Password to neo4j worked for us when loading a new Reactome database version for the first time.

You will be asked to create a new password

To change your password again:

:server change-password

7. View the Reactome database in the neo4j browser

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:

Try a Cypher command:

What sub-pathways are under under pathway, R-HSA-983169, Class I MHC mediated antigen processing & presentation?

8. Python interface to neo4j

More on the next page...

Copyright (C) 2018-present, DV Klopfenstein. All rights reserved.