Getting started with Docker

In this section we describe how to set up the Clinical Knowledge Graph from a Docker container. This container will install all the requirements needed, download source databases and build the CKG graph database, and open 5 ports through which to interact with the CKG.

To run the Docker, simply:

  1. Clone CKG’s repository: https://github.com/MannLabs/CKG

  2. Get licensed databases: https://ckg.readthedocs.io/en/latest/intro/getting-started-with-build.html#build-neo4j-graph-database

  3. Download the database dump and data directory from Mendeley:

            https://data.mendeley.com/public-files/datasets/mrcf7f4tc2/files/ 4. Extract compressed data file into the CKG folder and copy licensed databases in the right directories: - data/databases/{DrugBank|PhosphoSitePlus} - data/ontologies/SNOMED-CT 4. Build  thecontainer:

$ cd CKG/
$ docker build -t docker-ckg:latest .

  1. Run docker:

$ docker run -d --name ckgapp -p 7474:7474 -p 7687:7687 -p 8090:8090 -p 8050:8050 -v local_neo4j_logs_path:/var/log/neo4j -v local_ckg_directory_path:/CKG docker-ckg:latest

local_neo4j_logs_path: path where you want to store the neo4j logs

local_ckg_directory_path: path where CKG is installed

Once the docker is running:

  1. Access JupyterHub: http://localhost:8090/:

  • user:ckguser

  • password:ckguser

  1. Access Neo4j browser (connection may take several minutes): http://localhost:7474/

  2. Login using:

  • user: neo4j

  • password: NeO4J

When the database is running:

  1. In your web browser access CKG app: http://localhost:8050/

  2. Login using the test user:

  • user: test_user

  • password: test_user

  1. In the Home page navigate to the Admin page

  2. Run Minimal update (these can take a while but will run in the background. Follow progress in the docker dashboard logs)

  3. Explore options in CKG

Note

Be aware, this requires Docker to be previously installed.