System Requirements

The Clinical Knowledge Graph was conceived as a multi-user platform and therefore requires installation in a server-like setup and data systems administration knowledge. However, individual users can have local instances of the CKG, making sure data, software and hardware requirements are fulfilled.

Data

Licensed databases used by the CKG package require login and authentication in order to download their data. This is the case of SNOMED-CT, DrugBank and PhosphoSitePlus. Make sure you sign up to these three databases well in advance as the licensing process can take several days to conclude.

To sign up go to PSP Sign up, DrugBank Sign up and SNOMED-CT Sign up, and follow the instructions.

Once you have been given authorization to access the data, please download the files as follows:

  • PhosphoSitePlus: Acetylation_site_dataset.gz, Disease-associated_sites.gz, Kinase_Substrate_Dataset.gz, Methylation_site_dataset.gz, O-GalNAc_site_dataset.gz, O-GlcNAc_site_dataset.gz, Phosphorylation_site_dataset.gz, Regulatory_sites.gz, Sumoylation_site_dataset.gz and Ubiquitination_site_dataset.gz.

  • DrugBank: All drugs (under COMPLETE DATABASE) and DrugBank Vocabulary (under OPEN DATA).

  • SNOMED-CT: Download RF2 Files Now!.

These files will be later used in Build Neo4j graph database.

Software

  • Python 3.7.9

  • Redis server

  • Neo4j Desktop

  • Neo4j database == 4.2.3

Hardware

  • Memory: 16Gb

  • Disk space: >= 200Gb

  • Stable internet connection

Note

When building the Docker image further disk space is needed. We recomend allocating 300Gb, although the final CKG image will be around 150Gb.