https://github.com/knowledge-graph-hub/kg-microbe
https://github.com/knowledge-graph-hub/kg-microbe
anatomical-knowledge cell-shapes chebi chemicals data-modeling environments envo go knowledge-graph media metabolism microbiology named-entity-recognition ncbitaxonomy nlp oaklib phenotypes robot traits
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/knowledge-graph-hub/kg-microbe
- Owner: Knowledge-Graph-Hub
- License: bsd-3-clause
- Created: 2020-11-13T19:10:16.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2025-12-21T03:40:44.000Z (4 months ago)
- Last Synced: 2025-12-22T14:53:43.132Z (4 months ago)
- Topics: anatomical-knowledge, cell-shapes, chebi, chemicals, data-modeling, environments, envo, go, knowledge-graph, media, metabolism, microbiology, named-entity-recognition, ncbitaxonomy, nlp, oaklib, phenotypes, robot, traits
- Language: Jupyter Notebook
- Homepage: https://knowledge-graph-hub.github.io/kg-microbe/index.html
- Size: 518 MB
- Stars: 21
- Watchers: 3
- Forks: 4
- Open Issues: 184
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
Awesome Lists containing this project
README
# 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/).