KG-Microbe -- Knowledge graph construction for microbial traits and beyond

KG-Microbe preprint

Semantic Scholar

Documentation

latest KG-Microbe release

KG-Microbe @KG-Registry

Setup

• Install pipx
• Install poetry using pipx install poetry
• git clone https://github.com/Knowledge-Graph-Hub/kg-microbe.git
• cd kg-microbe
• poetry install

Download resources needed

• poetry run kg download : This will download the resources needed for this project.

Transform

• poetry run kg transform: This transforms the resources into knowledge graphs (KGs).

Merge

• poetry run kg merge: This merges all transformed graphs above.

Release

Requirements

In order to be able to make KG releases on this repository, you'll need:

• Appropriate permissions to this repository.
• A Github token that has permissions on this repository. This is how you set it in GitHub. Make sure your token has access to this project.
• Save this token locally assigned to the environemnt variable GH_TOKEN

  export GH_TOKEN = XXXX

  or add it to your ~/.bash_profile or ~/.bashrc file.

It should be noted that the KG construction process, particularly the transform step involving trimming of NCBI Taxonomy for any KG and the steps involving the microbial UniProt dataset for KG-Microbe-Function and KG-Microbe-Biomedical-Function, is computationally intensive. Successful execution on a local machine may require significant memory resources (e.g., >500 GB of RAM), further details can be found in the project's code repository.

Contributors

Please remember to run poetry run tox before every commit to make sure the code you commit is error-free.

Environment Variables

If you need to use environment variables for this project, copy .env.example to .env and set the environment variables accordingly:

cp .env.example .env

Then edit the .env file to configure the required environment variables for your setup.

Acknowledgements

This cookiecutter project was developed from the kg-cookiecutter template and will be kept up-to-date using cruft.