A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research,bioRxiv - Systems Biology

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A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research
bioRxiv - Systems Biology Pub Date : 2020-11-05 , DOI: 10.1101/2020.11.04.369041
Gergely Zahoránszky-Kőhalmi ₁ , Vishal B Siramshetty ₁ , Praveen Kumar _{2,

3} , Manideep Gurumurthy ₁ , Busola Grillo ₁ , Biju Mathew ₁ , Dimitrios Metaxatos ₁ , Mark Backus ₁ , Tim Mierzwa ₁ , Reid Simon ₁ , Ivan Grishagin _{1,

4} , Laura Brovold ₄ , Ewy A Mathé ₁ , Matthew D Hall ₁ , Samuel G Michael ₁ , Alexander G Godfrey ₁ , Jordi Mestres ₅ , Lars J Jensen ₆ , Tudor I Oprea _{2,

6,

7,

8}

Affiliation

Motivation: In the event of an outbreak due to an emerging pathogen, time is of the essence to contain or to mitigate the spread of the disease. Drug repositioning is one of the strategies that has the potential to deliver therapeutics relatively quickly. The SARS-CoV-2 pandemic has shown that integrating critical data resources to drive drug-repositioning studies, involving host-host, host-pathogen and drug-target interactions, remains a time-consuming effort that translates to a delay in the development and delivery of a life-saving therapy. Results: Here, we describe a workflow we designed for a semi-automated integration of rapidly emerging datasets that can be generally adopted in a broad network pharmacology research setting. The workflow was used to construct a COVID-19 focused multimodal network that integrates 487 host-pathogen, 74,805 host-host protein and 1,265 drug-target interactions. The resultant Neo4j graph database named "Neo4COVID19" is accessible via a web interface and via API calls based on the Bolt protocol. We believe that our Neo4COVID19 database will be a valuable asset to the research community and will catalyze the discovery of therapeutics to fight COVID-19. Availability: https://neo4covid19.ncats.io . Keywords: SARS-CoV-2, COVID-19, network pharmacology, graph database, Neo4j, data integration, drug repositioning

中文翻译：

催化网络药理学驱动的 COVID-19 研究的综合资源工作流程

动机：如果由于新出现的病原体而爆发，时间对于控制或减轻疾病的传播至关重要。药物重新定位是有可能相对快速地提供治疗的策略之一。SARS-CoV-2 大流行表明，整合关键数据资源以推动药物重新定位研究，包括宿主-宿主、宿主-病原体和药物-靶标相互作用，仍然是一项耗时的工作，这会导致开发和提供挽救生命的疗法。结果：在这里，我们描述了我们为快速出现的数据集的半自动集成而设计的工作流程，这些数据集通常可以在广泛的网络药理学研究环境中采用。该工作流程用于构建以 COVID-19 为重点的多模式网络，该网络集成了 487 种宿主病原体、74、805 种宿主-宿主蛋白和 1,265 种药物-靶点相互作用。生成的名为“Neo4COVID19”的 Neo4j 图形数据库可通过 Web 界面和基于 Bolt 协议的 API 调用进行访问。我们相信，我们的 Neo4COVID19 数据库将成为研究界的宝贵资产，并将促进发现抗击 COVID-19 的疗法。可用性：https://neo4covid19.ncats.io。关键词：SARS-CoV-2、COVID-19、网络药理学、图数据库、Neo4j、数据集成、药物重新定位我们相信，我们的 Neo4COVID19 数据库将成为研究界的宝贵资产，并将促进发现抗击 COVID-19 的疗法。可用性：https://neo4covid19.ncats.io。关键词：SARS-CoV-2、COVID-19、网络药理学、图数据库、Neo4j、数据集成、药物重新定位我们相信，我们的 Neo4COVID19 数据库将成为研究界的宝贵资产，并将促进发现抗击 COVID-19 的疗法。可用性：https://neo4covid19.ncats.io。关键词：SARS-CoV-2、COVID-19、网络药理学、图数据库、Neo4j、数据集成、药物重新定位

更新日期：2020-11-06

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