CovidGraph Website

COVID-19
Knowledge Graph

CovidGraph is a non-profit collaboration of researchers, software developers, data scientists and medical professionals.

We have built a research and communication platform that encompasses over 130,000 publications, case statistics, genes and functions, molecular data and much more.

Upcoming Events

In this short 30-minute webinar, Sebastian will demonstrate how CovidGraph can help researchers around the world to intuitively and visually navigate through the publications, genes, patents and more that make up our knowledge graph. Sebastian will go into detail about the custom visualization application, specifically designed to meet the needs of end users and built by yWorks in just a few days. He will further introduce you to the tools and frameworks used by the CovidGraph project and show you how you can reuse this knowledge in your own projects.

This webinar will start with a general introduction to the topic and the tools involved, and then briefly go into some technical aspects of the solution.

Sebastian Müller

CovidGraph Co-Initiator and Chief Technology Officer, yWorks

Sebastian has been working in the field of graph and diagram visualization for more than 20 years. Since 2002 he works as lead software architect and CTO at yWorks, dedicating his professional time on the yFiles diagramming libraries. In 2020, he co-initiated the CovidGraph project and created the first visualization app for the dataset.

Who Is This Project Aimed At?

Our aim is to help researchers quickly and efficiently find their way through COVID-19 datasets and to provide tools that use artificial intelligence, advanced visualization techniques, and intuitive user interfaces. This allows to explore papers, patents, existing treatments and medications around the family of the corona viruses.

In addition to literature data we connected information from fundamental entities in biology - namely genes and proteins and their function - , spanning a network of unparalleled size and knowledge.

Knowledge is primarily centered around the domain of corona-viruses but is steadily extended to other connected diseases.

Become part of this project and help free the world of COVID-19:

Medical & Pharma Researchers

Our main aim is to support you and enable your scientific analysis. Please feed us questions that you would like to ask of CovidGraph or take our apps and datasets for a test drive. We are relying on your input to create the applications that help you.

Medical
Databases

The CovidGraph project depends on data. We are looking for new datasources to enrich our knowledge graph. Any biomedical dataset relevant for COVID-19 research can be included in our database.

Data Scientists
& Developers

We welcome any development help you can offer. We manage our roadmap and development process with GitHub issues. You can find all information about our datasources, technologies and applications as well as guidance how to get started on GitHub.

GitHub

General Public,
Press & Media

We invite you to communicate and share our project. We are happy to answer your questions.

NEWS

News on CovidGraph

INTERVIEWNEW

As the year ends, we would like to introduce you to yet another member of our team: Martin Preusse, one of the co-founders of #CovidGraph

NEW

And right after that we directly send another video by Sebastian Müller and Jamie Munro. This one shows you how to select papers with similar gene combinations in #CovidGraph

NEW

Exporting selections as Cypher queries - watch this new short video done by Sebastian Müller and Jamie Munro

NEWPODCAST

Dr. Hairy’s Podcast deals with all kinds of topics of general medicine and general health. The NHS England initiators have just started a series of interviews with…

NEWTALK

Dr. Alexander Jarasch’s talk on “Connecting the dots in diverse data sets to combat diseases” at BiodataWorld Digital Congress last week, you can watch it here…

NEW

On our #CovidGraph website there is now a new section “News”, which Jakob Laenge from the Structr GmbH team has just completed.

The CovidGraph project is growing further – have a look at the updated diagram on the involved parties.

TALK

Dr. Alexander Jarasch is talking about “Connecting the dots in various data sets to combat disease - CovidGraph” at the BioData World Digital Congress.

Applications

The CovidGraph project provides a growing number of applications to interact with the data stored in the Knowledge Graph. Please feel free to use these apps free of charge, no registration/sign-up needed.

Visual Graph Explorer
Neo4j Browser

This application is provided by yWorks and allows you to explore the knowledge data in a visual way.

The Neo4j browser is a user interface for querying the graph directly on database level by pattern matching via Cypher. It offers a basic visualization of the result graph as well as data export and API access. A public version is available at:

HTTPS
https://db.covidgraph.org

User: public
Password: corona

Who we are

We are a diverse team of scientists, developers and data people from academia and industry.

TEAM PAGE

Datasets

We integrate data from various sources and link them in our knowledge graph:

COVID-19 Open Research Dataset (CORD-19)

In response to the COVID-19 pandemic, the Allen Institute for AI has partnered with leading research groups to prepare and distribute the COVID-19 Open Research Dataset (CORD-19), a free resource of over 44,000 scholarly articles, including over 29,000 with full text, about COVID-19 and the coronavirus family of viruses for use by the global research community.

https://pages.semanticscholar.org/coronavirus-research

The Lens COVID-19 Datasets

The Lens has assembled free and open datasets of patent documents, scholarly research works metadata and biological sequences from patents, and deposited them in a machine-readable and explorable form.

https://about.lens.org/covid-19/

Ensembl Genome Browser

Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

http://www.ensembl.org

NCBI Gene Database

Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.

https://www.ncbi.nlm.nih.gov/gene

The Gene Ontology Resource

The Gene Ontology (GO) knowledgebase is the world’s largest source of information on the functions of genes. This knowledge is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research.

http://geneontology.org

Experimental data from clinical studies and molecular genetics

(t.b.d.)

2019 Novel Coronavirus COVID-19 (2019-nCoV) Data Repository by Johns Hopkins CSSE

This is the data repository for the 2019 Novel Coronavirus Visual Dashboard operated by the Johns Hopkins University Center for Systems Science and Engineering (JHU CSSE). Also, Supported by ESRI Living Atlas Team and the Johns Hopkins University Applied Physics Lab (JHU APL).

https://github.com/CSSEGISandData/COVID-19

United Nations World Population Prospects 2019

The 2019 Revision of World Population Prospects is the twenty-sixth round of official United Nations population estimates and projections that have been prepared by the Population Division of the Department of Economic and Social Affairs of the United Nations Secretariat.

https://population.un.org/wpp/