kg-phenio

A graph for accessing and comparing knowledge concerning phenotypes across species and genetic backgrounds.

Also great for ontology-based graph machine learning experiments.

Setup

Clone the repository, then install with poetry install.

Download sources:

python run.py download

Transform sources:

python run.py transform

Build the merged graph:

python run.py merge

Prepare embeddings and classifiers with NEAT. These are defined in neat.yaml.

Or, if running locally, try using neat_local.yaml.

Name		Name	Last commit message	Last commit date
Latest commit History 419 Commits
.github/workflows		.github/workflows
kg_phenio		kg_phenio
notebooks		notebooks
ontoml_scripts		ontoml_scripts
post_setup		post_setup
tests		tests
.gitignore		.gitignore
Jenkinsfile		Jenkinsfile
LICENSE.txt		LICENSE.txt
README.md		README.md
download.yaml		download.yaml
generate_subgraphs.py		generate_subgraphs.py
graph_prefixcats.py		graph_prefixcats.py
merge.yaml		merge.yaml
neat.yaml		neat.yaml
poetry.lock		poetry.lock
pyproject.toml		pyproject.toml
run.py		run.py
sonar-project.properties		sonar-project.properties
tox.ini		tox.ini
transform-test.yaml		transform-test.yaml
transform.yaml		transform.yaml