NeDRexDB_v1 Archived

A quick way to set up a NeDRexDB_v1 instance using BioCypher and docker.

⚙️ Installation (local, for docker see below)

1. Clone this repository.

git clone git@github.com:repotrial/NeDRexDB_v1_Archive.git
cd NeDRexDB_v1_Archive

2. Configure the fields of the resulting knowledge graph. Can be found in scripts.nedrex_script.py

🐳 Run Docker

This repo also contains a docker compose workflow to create the NeDRexDB_v1 using BioCypher and load it into a dockerized Neo4j instance automatically. To run it, simply execute docker compose up -d (or docker-compose up -d) in the root directory of the project. This will build and start up a single (detached) docker container with a Neo4j instance that contains the NeDRexDB_v1 knowledge graph built by BioCypher as the DB nedrex, which you can connect to and browse at localhost:7474 (don't forget to switch the DB to nedrex instead of the standard neo4j). Authentication is set to neo4j/neo4jpassword by default and can be modified in the docker-variables.env file.

Alternative

You can pull a prebuilt version of the NeDRex-Archive from dockerhub by using the docker-compose.prebuilt.yml docker-compose file as follows:

docker-compose -f docker-compose.prebuilt.yml up -d