Monarch Ingest

Overview

The Monarch Ingest generates KGX formatted files conforming to the BioLink Model from a wide variety of biomedical data sources.

The eventual output of the Monarch Ingest process is the Monarch KG.
The latest version of this can be found at data.monarchinitiative.org

Monarch Ingest is managed with uv, which creates and manages its own virtual environment.

monarch-ingest is a Python 3.10+ package, managed with uv.

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

curl -LsSf https://astral.sh/uv/install.sh | sh

Clone the repo:

git clone git@github.com:monarch-initiative/monarch-ingest

(Optional) Activate the virtual environment:

# This step removes the need to prefix all commands with `uv run`
source .venv/bin/activate

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, gcor 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
```
Upload the results to the Monarch Ingest Google bucket
```
ingest release
```