AlzKB (http://alzkb.ai/)

A knowledge base for AI research in Alzheimer Disease, based on graph databases.

Authors

AlzKB is designed and developed by the following authors (in alphabetical order):

• Britney Graham, PhD (Cedars-Sinai)
• Yun Hao, MS (UPenn)
• Rachit Kumar (UPenn)
• Xi Li, MD (Cedars-Sinai)
• Nick Matsumoto (Cedars-Sinai)
• Jason H. Moore, PhD, FACMI (Cedars-Sinai)
• Marylyn Ritchie, PhD (UPenn)
• Joseph D. Romano, PhD (UPenn)
• Li Shen, PhD, FAIMBE (UPenn)
• Van Truong, MS (UPenn)
• Mythreye Venkatesan, MS (Cedars-Sinai)
• Paul Wang, PhD (Cedars-Sinai)

Prerequisites

• Python (version 3.7 or later)
• Instance of Neo4j with n10s (v4.2 or greater) plugin installed

Installation

To build a copy of AlzKB's graph database, you can either:

• Download a dump of the Neo4j database and import it into Neo4j

• Build the knowledge base from its original third-party sources and populate an empty Neo4j graph database

Install from database dump (easy)

• Before doing anything else, make sure you have an up-to-date version of Neo4j installed on the new database server. This can be Neo4j Desktop or Neo4j Server, depending on your intended use.

• Visit the Releases page and find the version of AlzKB you want to install. Unless you have a particular reason to do otherwise, this should probably be the most recent release. Follow the link in the release notes to the corresponding database dump (it will redirect to an external page).

• Once you have downloaded the dump, extract the archive.

• If you haven't already done so, create an empty database in Neo4j.

• Stop any running Neo4j database instances (you can only import the dump when the destination database is shut down).

• Use the neo4j-admin utility (included with Neo4j) to import the database from the dump. You may need to add the program to your PATH variable or similar; if using Neo4j Desktop you can open a terminal window from within the application and use cd bin to access the directory where the neo4j-admin program is located. (If you are installing on Neo4j Server the following command needs to be run by the appropriate user; this is often neo4j) Assuming that neo4j-admin is accessible in your current directory, an example import command for UNIX-based operating systems could look like this (substitute database name and dump location as needed):

  $ neo4j-admin load --verbose --force --database=neo4j --from=~/Downloads/alzkb.dump

• Start the Neo4j database and open it to verify everything looks good.

Build from scratch (less easy)

For detailed instructions on building AlzKB from scratch, see here

Start by installing the Python package, which includes the necessary scripts:

$ git clone https://github.com/EpistasisLab/AlzKB
$ cd AlzKB
$ pip install .

Download the third-party database sources

First, install MySQL and make sure it is running, as some of the source databases are only available as MySQL dumps.

We've created a script that will fetch all of the source files and put them into the expected directory structure. We will try to keep this script as updated as possible, but if you encounter any issues we suggest looking at the script and making sure it points to entities that still exist.

$ alzkb bootstrap

Populate the ontology

We use the external ista library to populate the OWL ontology. This should be pretty much entirely automated:

$ alzkb build

Load the ontology contents into Neo4j

This script will import the OWL 2 ontology contents into an empty Neo4j database and clean up unnecessary artifacts left over by the OWL 2 standard:

$ alzkb install

After this, check the Neo4j database (which will now be turned on) and make sure everything looks alright.