BioCypher meta-graph

Information about pipelines and adapters available in BioCypher, as described on the GitHub Projects board for Components. Uses the GitHub API adapter to populate the graph and mount it on localhost:7474 using the Neo4j docker container. To run locally, you will need to have Docker installed and running. Then, you can run it using:

git clone https://github.com/biocypher/meta-graph.git
cd meta-graph
docker compose up -d

After the graph has been built, you can access it in the Neo4j Browser at http://localhost:7474. This version of the meta-graph is a read-only instance, so you will not be able to make changes to the graph. Authentication is not required. To see the entire graph, you can run the following Cypher query:

MATCH (n) RETURN n

The online version is available at https://meta.biocypher.org/. In the online version, no authentication is required (simply click on 'Connect').

Docker Compose

The docker-compose.yml file is used to build the graph. It uses the three stages build, import, and deploy to serve the graph from Neo4j. The deploy stage is necessary because a read-only graph cannot be served from the import stage container. If you want to locally create a read-write instance, you can simply change the docker-compose.yml file to enable writing by setting NEO4J_dbms_databases_default__to__read__only in the deploy stage to false.

There is a simpler, one-stage setup that allows read-write in the simple-docker branch of this repository.

Stages

• build: Builds the graph from the GitHub API. This stage runs BioCypher and creates the knowledge graph in the configured build directory (mounted as a volume to the docker compose).
• import: Imports the graph from the build directory into Neo4j. This stage runs the Neo4j docker container and imports the graph from the build directory into the Neo4j database. The database is started once and stopped again to perform first-time setup of Neo4j.
• deploy: Serves the graph from Neo4j. This stage runs the Neo4j docker container (again) and serves the graph from the Neo4j database. The database is started in read-only mode.