Monkeypox Knowledge Graph: A comprehensive representation embedding chemical entities and associated biology of Monkeypox

  public model
Model Identifier
MODEL2208040001
Short description
We collected and rationally assembled several biological study results, assays, drug candidates, and preclinical evidence to form a dynamic and comprehensive network. In this process, we used active chemicals from PubChem and ChEMBL. The proteins were fetched from Uniprot (MPXV) and DISEASES (Humans). The KG is compliant with FAIR annotations allowing seamless transformation and integration to/with other formats and infrastructures. Please check the github for more details: https://github.com/Fraunhofer-ITMP/mpox-kg
Format
Python (3.6)
Related Publication
  • Monkeypox Knowledge Graph: A comprehensive representation embedding chemical entities and associated biology of Monkeypox
  • Reagon Karki, Yojana Gadiya, Andrea Zaliani, Philip Gribbon
  • Biorxiv , 8/ 2022 , DOI: 10.1101/2022.08.02.502453
  • 1. Discovery Research ScreeningPort, Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany 2. Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590 Frankfurt, Germany
  • The outbreak of Monkeypox virus (MPXV) infection in May 2022 is declared a global health emergency by WHO. As of 28th July, 21067 cases have been confirmed and the numbers are on the rise. Unfortunately, MPXV pathophysiology and its underlying mechanisms are not yet understood. Likewise, the knowledge of biochemicals and drugs used against MPXV and their downstream effects is sparse. In this work, using Knowledge Graph (KG) representations we have depicted chemical and biological aspects of MPXV. To achieve this, we have collected and rationally assembled several biological study results, assays, drug candidates, and preclinical evidence to form a dynamic and comprehensive network. The KG is compliant with FAIR annotations allowing seamless transformation and integration to/with other formats and infrastructures.
Contributors
Submitter of the first revision: Reagon Karki
Submitter of this revision: Reagon Karki
Modellers: Reagon Karki

Metadata information


Curation status
Non-curated

Modelling approach(es)
Other

Tags

Connected external resources

Name Description Size Actions

Model files

Monkeypox_KG.pkl Monkeypox KG created with pybel framework 6.19 MB Preview | Download

Additional files

Monkeypox_KG.csv Monkeypox KG exported as triples in csv format 7.90 MB Preview | Download
Monkeypox_KG.graphml Monkeypox KG file for cytoscape visualization 11.01 MB Preview | Download
Monkeypox_KG.sif Monkeypox KG exported as triples in sif format 2.73 MB Preview | Download

  • Model originally submitted by : Reagon Karki
  • Submitted: Aug 4, 2022 10:28:34 AM
  • Last Modified: Aug 4, 2022 10:28:34 AM
Revisions
  • Version: 1 public model Download this version
    • Submitted on: Aug 4, 2022 10:28:34 AM
    • Submitted by: Reagon Karki
    • With comment: Import of Monkeypox Knowledge Graph: A comprehensive representation embedding chemical entities and associated biology of Monkeypox