biolink/kgx repository overview

⁠KGX

KGX (Knowledge Graph Exchange) is a Python library and set of command line utilities for exchanging Knowledge Graphs (KGs) that conform to or are aligned to the Biolink Model.

⁠KGX in a container

KGX can be run from within a container. This reduces the chance of running into any dependency or environment issues.

⁠Starting a container

To start a container,

docker run -it biolink/kgx:latest

You can use the environment in the container as a sandbox for running KGX.

To start a container in a detached mode,

docker run -itd biolink/kgx:latest

To invoke KGX CLI from outside the container,

docker exec -it <CONTAINER ID> kgx --help

To run KGX on your files you should first mount volumes to the container such that files and folders on the host is visible to the container,

docker run -itd -v /your/data/folder/input_data:/input_data -v /your/data/folder/output_data:/output_data biolink/kgx:latest