KaBOB installation (Virtuoso) not ready for use

Note, the Virtuoso build is still in development. It is not ready for use. This page is simply a placeholder and will be updated when the Virtuoso build development is complete.

How to install KaBOB using Virtuoso as a backend

Virtuoso Build Setup

Edit the virtuoso/build/config/virtuoso.ini file to specify the available resources on your system. Specifically, see lines 86-117. By default, 32GB of RAM is assumed to be available on the host machine. If this number needs to be modified (either higher or lower), then comment out lines 104-105 and uncomment the appropriate two lines for the host system.

At this point, the KaBOB build is ready to proceed via a succession of scripts that call Docker commands. All scripts should be run from the base directory of the project: cd kabob.app.git

VIRTUOSO BUILD STEP 1: Download data sources and generate RDF

The first step of the build downloads a collection of publicly available data sources and subsequently generates RDF versions of these sources that are grounded in classes defined in an extension of the Information Artifact Ontology. Optionally, the user can also provide the local path to some data sources which are not directly downloadable (often due to licensing restrictions).

Run:

scripts/step1_rdf-gen.sh -k [KEY] -c [n] -d [DRUGBANK_XML_FILE] -p [PHARMGKB_RELATIONSHIPS_FILE]

where:

• [KEY] is a user-defined key to uniquely identify the KaBOB build. This key enables multiple KaBOB instances to be run in the same Docker environment. Example keys may be "development" or "production". Keys must not contain whitespace.
• [n] is the number of docker containers (1-5) that will be used to generate RDF. n should be <= the number of cores available on your machine.
• [DRUGBANK_XML_FILE] is the path to the DrugBank 'full database.xml' file on the local file system. The DrugBank 'full database.xml' file can be downloaded from here after creating an account and agreeing to the DrugBank license. This argument is optional. If the user prefers to exclude DrugBank from the KaBOB build then this argument can be excluded.
• [PHARMGKB_RELATIONSHIPS_FILE] is the path to the PharmGKB relationships file (relationships.tsv) on the local file system. Use of this file requires a PharmGKB license which can be obtained here. Note: This argument is optional. If the user prefers to exclude the PharmGKB relationships from the KaBOB build then this argument can be excluded.

This step may take >90 min.

VIRTUOSO BUILD STEP 2: Setup and start Virtuoso

Run: scripts/virtuoso-specific-scripts/step2_virtuoso-setup.sh -k [KEY] where:

• [KEY] is the same user-defined key specified in Build Step 1 above that uniquely identifies the KaBOB build.

At this point, Virtuoso should be running and its Web Conductor UI should be visible at http://[HOST_URL]:8890, where [HOST_URL] is the URL for the machine hosting KaBOB. Access credentials for logging into Virtuoso are dba/dba by default.

VIRTUOSO BUILD STEP 3: Build KaBOB

Run: scripts/virtuoso-specific-scripts/step3_build-kabob.sh -k [KEY] where:

• [KEY] is the same user-defined key specified in Build Step 1 above that uniquely identifies the KaBOB build.

Building the human KaBOB instance should take ~100 minutes. If you would like to follow along via the agraph logs you can login to the agraph container using docker exec -ti agraph bash and then view the agraph log output using tail -f /tmp/agraph_load_check---supervisor-MKGnli.log (note the name of the log file may be slightly different)