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bill-baumgartner edited this page Jun 27, 2017 · 3 revisions

kabob.app

Install, build, and run a KaBOB instance via Docker

The KaBOB Knowledge Base Of Biology

The KaBOB Knowledge Base of Biology is a formal integration of biological knowledge using Semantic Web standards. Its knowledge is grounded in the community-curated Open Biomedical Ontologies, and it uses this ontological foundation to integrate information mined from a collection of biomedical databases with a concerted effort to model biology separate from database content. More information about KaBOB is available at the KaBOB GitHub page. The original publication describing KaBOB in detail is:

KaBOB: Ontology-Based Semantic Integration of Biomedical Databases
Kevin M Livingston, Michael Bada, William A Baumgartner Jr., and Lawrence E Hunter
BMC Bioinformatics. 2015 Apr 23;16:126. doi: 10.1186/s12859-015-0559-3. PubMedId:25903923

The kabob.app project facilitates the installation and construction of a KaBOB instance via Docker.

Caveats

  1. This project is set up to build an instance of KaBOB based on human data. Future extensions of this project will parameterize the species on which KaBOB instances can be based.

NOTE: In the text below, 'host machine' refers to the machine that will host your KaBOB instance.

System requirements for the host machine

  • Unix-based OS (the scripts in this project assume availability of a bash shell)
  • The more RAM the better. [TODO: determine reasonable minimums for RAM usage]

Pre-installation

  1. Install Docker on the machine that will host KaBOB

  2. Clone the kabob.app repository to the host machine:

    git clone --branch v0.3 https://github.com/bill-baumgartner/kabob.app ./kabob.app.git

  3. There are a few data sources that cannot be automatically downloaded due to licensing restrictions. If you would like the following data sources to be included in your KaBOB instance, please follow the instructions for each below and save the downloaded file(s) to the host machine.

  • DrugBank
    • Requires an account to download. Please note the license restrictions.
    • Download and unzip this file to obtain the full database.xml file.
  • PharmGKB
    • To access the PharmGKB Variant, Gene and Drug Relationship Data you must submit a license request.
    • Obtain the relationships.tsv file

KaBOB installation

Your KaBOB instance will be hosted in a triple-store and the installation steps are semi-specific to the triple-store vendor you choose to use. Below is a list of wiki pages that detail how to install KaBOB for a given triple-store vendor.

Clone this wiki locally