KG-Microbe - Building Modular and Scalable Knowledge Graphs for Microbiome and Microbial Sciences

 # KG-Microbe -- Knowledge graph construction for microbial traits and beyond [KG-Microbe preprint](https://www.biorxiv.org/content/10.1101/2025.02.24.639989v1) [Semantic Scholar](https://www.semanticscholar.org/paper/KG-Microbe%3A-A-Reference-Knowledge-Graph-and-for-joachimiak-Hegde/c49a7ed4e5e1c0db815a3b185148877d914473f2) [Documentation](http://kghub.org/kg-microbe/index.html) [latest KG-Microbe release](https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/tag/2025-03-07) [KG-Microbe @KG-Registry](https://kghub.org/kg-registry/resource/kg-microbe/kg-microbe.html) # Setup - Install [pipx](https://pipx.pypa.io/stable/installation/) - 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](https://docs.github.com/en/organizations/managing-programmatic-access-to-your-organization/setting-a-personal-access-token-policy-for-your-organization#restricting-access-by-personal-access-tokens-classic). Make sure your token has access to this project. - Save this token locally assigned to the environemnt variable `GH_TOKEN` ```shell 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: ```shell cp .env.example .env ``` Then edit the `.env` file to configure the required environment variables for your setup. # Acknowledgements This [cookiecutter](https://cookiecutter.readthedocs.io/en/stable/README.html) project was developed from the [kg-cookiecutter](https://github.com/Knowledge-Graph-Hub/kg-cookiecutter) template and will be kept up-to-date using [cruft](https://cruft.github.io/cruft/).