Covid-19 Dataset Search

This repository contains the source code used to create the Covid-19 AI-powered search. The data in the website comes from the COVID-19 Open Research Dataset Challenge (CORD-19) Kaggle challenge. This website uses our AI-enabled graph and search technology to enable you to explore the dataset using machine-learning-based synonyms and find similar papers using word and graph embeddings. You can check more details on our accompanying blog post.

The code here is used to ingest the data in the back-end Mosaik instance, and to build the front-end that renders each of the data types in the system.

To run the data ingestion, download the dataset, unzip it to a folder, and then run the data ingestion project with the following arguments:

git clone https://github.com/curiosity-ai/covid-19/
cd covid-19
cd data-ingestion
dotnet run papers --server https://covid.curiosity.ai/api/ --token {AUTH_TOKEN} --folder {PATH_TO_DATA}

This script will create the required nodes & edges on the graph, and create the relationships between papers, authors, institutions & locations.

To build and publish the front-end project, we recomend you to install our CLI tool:

dotnet tool install mosaik.cli --global

You can test the front-end locally by building the front-end project, and then running the following from the base folder of this repository:

cd covid-19
mosaik serve --server https://covid.curiosity.ai/api/ --folder .\bin\Debug\net461\bridge\

Note: Building the front-end project using the dotnet build command is not yet supported. You can either install the Bridge.Net CLI, or build the project on Visual Studio.

Disease Ontology (new✨)

The Disease Ontology is a community driven, open source ontology that is designed to link disparate datasets through disease concepts. It provides a computable structure of inheritable, environmental and infectious origins of human disease to facilitate the connection of genetic data, clinical data, and symptoms through the lens of human disease. For more info, visit the project website here.

To ingest the disease ontology, download the doid.json file from the Human Disease Ontology project's repository, and run the following command:

git clone https://github.com/curiosity-ai/covid-19/
cd covid-19
cd data-ingestion
dotnet run diseases --server https://covid.curiosity.ai/api/ --token {AUTH_TOKEN} --folder {PATH_TO_DOID.JSON}

Acknowledgements

The dataset used in the website was created by the Allen Institute for AI in partnership with the Chan Zuckerberg Initiative, Georgetown University’s Center for Security and Emerging Technology, Microsoft Research, and the National Library of Medicine - National Institutes of Health, in coordination with The White House Office of Science and Technology Policy.

The online site and this repository, are provided free of charge, without any warranty, either expressed or implied. Licenses for the underlying papers are noted in the individual references.

The Disease Ontology is a project of the Institute of Genome Sciences, from the University of Maryland School of Medicine.

If you want your own account to explore the data, access to a free developer license of our system, or any other information, get in touch under [email protected] or follow us on twitter.