猴痘知识图谱：一种全面的表示，嵌入了猴痘的化学实体及相关生物学信息。

Mpox Knowledge Graph: a comprehensive representation embedding chemical entities and associated biology of Mpox.

作者信息

Karki Reagon, Gadiya Yojana, Zaliani Andrea, Gribbon Philip

机构信息

Discovery Research ScreeningPort, Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany.

Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590 Frankfurt, Germany.

出版信息

Bioinform Adv. 2023 Apr 3;3(1):vbad045. doi: 10.1093/bioadv/vbad045. eCollection 2023.

DOI:10.1093/bioadv/vbad045

PMID:37187795

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10181838/

Abstract

SUMMARY

The outbreak of Mpox virus (MPXV) infection in May 2022 is declared a global health emergency by WHO. A total of 84 330 cases have been confirmed as of 5 January 2023 and the numbers are on the rise. The MPXV pathophysiology and its underlying mechanisms are unfortunately 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 pre-clinical 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.

AVAILABILITY AND IMPLEMENTATION

The programmatic scripts for Mpox KG are publicly available at https://github.com/Fraunhofer-ITMP/mpox-kg. It is hosted publicly at https://doi.org/10.18119/N9SG7D.

SUPPLEMENTARY INFORMATION

Supplementary data are available at online.

摘要

2022年5月爆发的猴痘病毒（MPXV）感染被世界卫生组织宣布为全球卫生紧急事件。截至2023年1月5日，共确诊84330例病例，且数量仍在上升。遗憾的是，猴痘病毒的病理生理学及其潜在机制尚不清楚。同样，针对猴痘病毒使用的生化物质和药物及其下游效应的知识也很匮乏。在这项工作中，我们使用知识图谱（KG）表示法描绘了猴痘病毒的化学和生物学方面。为实现这一目标，我们收集并合理整合了多个生物学研究结果、检测方法、候选药物和临床前证据，以形成一个动态且全面的网络。该知识图谱符合FAIR注释，允许与其他格式和基础设施进行无缝转换和集成。