Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Oct 14;38(20):4843-4845.
doi: 10.1093/bioinformatics/btac592.

CovidGraph: a graph to fight COVID-19

Lea Gütebier  1   2 , Tim Bleimehl  2   3 , Ron Henkel  1 , Jamie Munro  2 , Sebastian Müller  2 , Axel Morgner  2 , Jakob Laenge  2 , Anke Pachauer  2 , Alexander Erdl  2 , Jens Weimar  2 , Kirsten Walther Langendorf  2 , Vincent Vialard  2 , Thorsten Liebig  2 , Martin Preusse  2 , Dagmar Waltemath  1 , Alexander Jarasch  2   3
Affiliations

CovidGraph: a graph to fight COVID-19

Lea Gütebier et al. Bioinformatics. .

Abstract

Summary: Reliable and integrated data are prerequisites for effective research on the recent coronavirus disease 2019 (COVID-19) pandemic. The CovidGraph project integrates and connects heterogeneous COVID-19 data in a knowledge graph, referred to as 'CovidGraph'. It provides easy access to multiple data sources through a single point of entry and enables flexible data exploration.

Availability and implementation: More information on CovidGraph is available from the project website: https://healthecco.org/covidgraph/. Source code and documentation are provided on GitHub: https://github.com/covidgraph.

Supplementary information: Supplementary data is available at Bioinformatics online.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Screenshot of Neo4j Bloom with semi-natural language query ‘Is there a model for a corona virus gene?’. This figure shows the shortest path between the systems biology model ‘Gulbudak2019.1—Heterogeneous viral strategies promote coexistence in virus-microbe systems (Lytic)’ (cyan, BioModels, BIOMD0000000845) by Gulbudak and Weitz (2019) which is connected to MaSyMoS_Reaction (light green), MaSyMoS_Annotation (ochre), MaSyMoS_Resource (green) to the Gene Ontology term ‘Virus entry into host cell’ (blue, GO: 0019063) which, in turn, is associated with the protein Q9BYF1 (plum, UniProt) coded by the transcript ENST00000427411 (pink, RefSeq) of the corona virus gene ACE2 (orange, GenBank, ENSG00000130234) (A color version of this figure appears in the online version of this article.)
See this image and copyright information in PMC

References

    1. Cowell L.G., Smith B. (2010). Infectious disease ontology. In: Sintchenko, V. (ed) Infectious Disease Informatics. Springer, New York, pp. 373–395. https://doi.org/10.1007/978-1-4419-1327-2_19.
    1. Dong E. et al. (2020) An interactive web-based dashboard to track COVID-19 in real time. Lancet. Infect. Dis., 20, 533–534. - PMC - PubMed
    1. Gulbudak H., Weitz J.S. (2019) Heterogeneous viral strategies promote coexistence in virus-microbe systems. J. Theor. Biol., 462, 65–84. - PubMed
    1. Gütebier L. et al. (2021) COVIDGraph: connecting biomedical COVID-19 resources and computational biology models. In: 2nd Workshop on Search, Exploration, and Analysis in Heterogeneous Datastores, SEA-Data 2021. pp. 34–37.
    1. Heldt F.S. et al. (2012) Modeling the intracellular dynamics of influenza virus replication to understand the control of viral RNA synthesis. J. Virol., 86, 7806–7817. - PMC - PubMed

Publication types