IFX_ODIN

Ontology and Data Integration Network

We are currently enhancing our data integration capabilities (NCATS and other open-source biomedical datasets) by transitioning from traditional relational databases to an interoperable graph database, structured around the BioLink Data Model, https://github.com/ncats/IFX_ODIN. This integration seamlessly incorporates comprehensive gene/protein information, disease associations, and drug data, enabling more advanced AI/ML applications. A public graph database is coming soon.For more information about our initiatives or to collaborate, please contact Jessica Maine or Keith Kelleher

make virtual environment

• python -m venv .venv
• source .venv/bin/activate
• export PYTHONPATH=/Users/kelleherkj/IdeaProjects/NCATS_ODIN:$PYTHONPATH
  • update with your correct path
• install dependencies in your python environment
  • pip install -r requirements.txt

start local memgraph

• navigate to the container
• docker compose up -d
  • if you already have memgraph running locally, you can update the ports in the docker-compose.yml file so they don't clash
    • "7474:7474" # update the first numbers to something else i.e. "27474:7474"
    • "7687:7687" # i.e. "27687:7687"
• point your browser to "http://localhost:7474" (or the port you mapped i.e. 27474)
• point your bolt address to the other one
• successfully see your graph

save your credentials into "src/use_cases/secrets/local_credentials.yaml"

url: bolt://localhost:7687
user: neo4j
password: password