Covid-19-Community

This project is a community effort to build a Neo4j Knowledge Graph (KG) that links heterogenous data about COVID-19 to help fight this outbreak! It serves as a sandbox and incubator project and the best ideas will be incorporated into the Covid-19-Net KG.

Join "GraphHackers, Let’s Unite to Help Save the World — Graphs4Good 2020".

What kind of data can you contribute? Here are some of our ideas.

How can you contribute?

• File an issue to discuss your idea so we can coordinate efforts

• We need your help with specific issues

• Suggest publically accessible data sets

• Suggest graph queries to gain new insights from the KG

• Add Jupyter Notebooks with data analyses

• Add data and map visualizations

• Help improve the data model

• Report bugs or issues

How to use this project?

You can run the Jupyter Notebooks in this repo in your web browser:

Once Jupyter Lab launches, navigate to the notebooks folder and run the following notebooks:

• 1a-Strains.ipynb (downloads the latest SARS-CoV-2 strain data and creates node and relationship files in the data folder)

• 1b-... (create notebooks that add new node and relationship files)

• 2-CreateKnowledgeGraph (creates a Neo4j Knowledge Graph by batch-uploading the nodes and relationships)

• 3-ExampleQueries (runs Cypher queries on the Knowledge Graph)

A prototype Subgraph that represents relationships for Virus Strains

This subgraph maps the relationships between the Pathogen that causes the Outbreak, the strains of the virus, the host (human or animal), and the locations where it was found.

How to run this project locally

1. Fork this project

A fork is a copy of a repository in your GitHub account. Forking a repository allows you to freely experiment with changes without affecting the original project.

In the top-right corner of this GitHub page, click Fork.

Then, download all materials to your laptop by cloning your copy of the repository, where your-user-name is your GitHub user name. To clone the repository from a Terminal window or the Anaconda prompt (Windows), run:

git clone https:/your-user-name/covid-19-community.git
cd covid-19-community

2. Create a conda environment

The file environment.yml specifies the Python version and all packages required by the tutorial.

conda env create -f environment.yml

Activate the conda environment

conda activate covid-19-community

3. Install Neo4j Desktop

Download Neo4j

Then, launch the Neo4j Browser, create an empty database, and set the password to "neo4jbinder"

4. Set Environment Variable

Set a NEO4J_HOME environment variable with the path to the database installation.

(Example path from Mac OS: /Users/username/Library/Application Support/Neo4j Desktop/Application/neo4jDatabases/database-993db298-6374-4f0a-9a9a-d0783480877a/installation-3.5.14)

5. Launch Jupyter Lab

jupyter lab

6. Browse KG in Neo4j Browser

After you create the graph database by running the Jupyter Notebooks, start the database in Neo4j Browser to interactively explore the KG.