bio-data-harmoniser

Automatically ingest and harmonise biological data from different sources.

About

Biomedical data is messy and disharmonised. This tool aims to help researchers ingest and harmonise biological data from different sources, to make it easier to get insights from the data.

Usage

In general, we recommend using Docker to run the tool. To do so, you first need to ingest the Monarch KG ontology:

make ingest_ontology_in_docker

Then, you can run the tool:

make run_in_docker

This will start the tool in a Docker container. You can access the tool at http://0.0.0.0:3000.

Note: since the ingestion of the ontology also computes the embeddings for the entities, it can take a while. If you have a GPU available, we recommend using it by setting the LLM_EMBEDDINGS_DEVICE environment variable to cuda when running make ingest_ontology_in_docker.