Ondex data integration platform for building knowledge networks.
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README.md

Ondex-KnetBuilder

Ondex components and applications that are necessary for building genome-scale knowledge networks used in projects like KnetMiner. It includes the Ondex base, CLI, workflow engine and a set of plugins (parsers, mappers, transformers, filters and exporters) that are relevant for building genome-scale knowledge networks as described in Hassani-Pak et al. 2016.

Requirements

  • Java 8

Downloads

Execution

  1. Create a new folder e.g. mkdir knetbuilder-folder

  2. Download the latest KnetBuilder release and unzip in knetbuilder-folder

  3. Download the tutorial files and unzip in knetbuilder-folder

  4. Check the folder structure looks like this

-bash-4.1$ ls knetbuilder-folder/
ondex-mini-1.2
tutorial_files
  1. Go to the downloaded ondex-mini folder and run a workflow:
cd ondex-mini-1.2
./runme.sh ../tutorial_files/Workflow/HumanDiseaseKNET.xml
  1. The KnetBuilder workflow integrates several datasets and creates a OXL file tutorial_files/NeuroDiseaseKnet.oxl

  2. The OXL file can be opened in the Ondex Desktop application or explored in the KnetMiner web application

Documentation

We keep most of our documentation on this repository's Wiki (note that there are many links on the right column in that page).