KG-Alzheimers

Overview

KG-Alzheimers generates KGX formatted files conforming to the BioLink Model from a wide variety of biomedical data sources focused on Alzheimer's disease.

The eventual output of the KG-Alzheimers process is the Alzheimer's Knowledge Graph.
The latest version can be found at kghub.io.

KG-Alzheimers is built using Poetry, which will create its own virtual environment.

Installation

kg-alzheimers is a Python 3.8+ package, installable via Poetry.

Install Poetry, if you don't already have it:

curl -sSL https://install.python-poetry.org | python3 -

# Optional: Have poetry create its venvs in your project directories
poetry config virtualenvs.in-project true

Clone the repo and build the code:

git clone git@github.com:Knowledge-Graph-Hub/kg-alzheimers.git

Install kg-alzheimers:
```
cd kg-alzheimers
poetry install
```

(Optional) Activate the virtual environment:

# This step removes the need to prefix all commands with `poetry run`
poetry shell

Usage

For a detailed tutorial on ingests and how to make one, see the Create an Ingest tab.

CLI usage is available in the CLI tab, or by running ingest --help.

Run the whole pipeline!

Download the source data:
```
ingest download --all
```
Run all transforms:
```
ingest transform --all
```
Merge all transformed output into a tar.gz containing one node and one edge file
```
ingest merge
```
(Optional) Generate closure-enriched denormalized tables and prepare release artifacts
```
ingest closure
ingest prepare-release
```
(CI only) Artifact publication to S3 is automated by Jenkins (Jenkinsfile); the local ingest release command now emits a deprecation notice.