KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response.

Justin ReeseChristopher J Mungall


Integrated, up-to-date data about SARS-CoV-2 and COVID-19 is crucial for the ongoing response to the COVID-19 pandemic by the biomedical research community. While rich biological knowledge exists for SARS-CoV-2 and related viruses (SARS-CoV, MERS-CoV), integrating this knowledge is difficult and time-consuming, since much of it is in siloed databases or in textual format. Furthermore, the data required by the research community vary drastically for different tasks; the optimal data for a machine learning task, for example, is much different from the data used to populate a browsable user interface for clinicians. To address these challenges, we created KG-COVID-19, a flexible framework that ingests and integrates heterogeneous biomedical data to produce knowledge graphs (KGs), and applied it to create a KG for COVID-19 response. This KG framework also can be applied to other problems in which siloed biomedical data must be quickly integrated for different research applications, including future pandemics.


Dec 26, 2001·Nucleic Acids Research·X ChenY Z Chen
May 17, 2005·Genome Biology·Barry SmithCornelius Rosse
Oct 28, 2008·American Journal of Human Genetics·Peter N RobinsonStefan Mundlos
Sep 29, 2011·Nucleic Acids Research·Anna GaultonJohn P Overington
Jul 5, 2013·Methods in Molecular Biology·Caroline F ThornRuss B Altman
Nov 16, 2013·Nucleic Acids Research·Sandra OrchardHenning Hermjakob
Jun 28, 2016·Nature Reviews. Microbiology·Emmie de WitVincent J Munster
Oct 30, 2016·Nucleic Acids Research·Oleg UrsuTudor I Oprea
Nov 18, 2016·KDD : Proceedings·Aditya Grover, Jure Leskovec
Oct 30, 2018·Nucleic Acids Research·Oleg UrsuTudor Oprea
Nov 30, 2019·Nature Communications·Dmitry Kobak, Philipp Berens
Mar 21, 2020·Cell Discovery·Yadi ZhouFeixiong Cheng
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