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2019冠状病毒病本体论

The COVID-19 Ontology.

作者信息

Sargsyan Astghik, Kodamullil Alpha Tom, Baksi Shounak, Darms Johannes, Madan Sumit, Gebel Stephan, Keminer Oliver, Jose Geena Mariya, Balabin Helena, DeLong Lauren Nicole, Kohler Manfred, Jacobs Marc, Hofmann-Apitius Martin

机构信息

Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53754 Sankt Augustin, Germany.

Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, 53113 Bonn, Germany.

出版信息

Bioinformatics. 2021 Apr 5;36(24):5703-5705. doi: 10.1093/bioinformatics/btaa1057.

DOI:10.1093/bioinformatics/btaa1057
PMID:33346828
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7799333/
Abstract

MOTIVATION

The COVID-19 pandemic has prompted an impressive, worldwide response by the academic community. In order to support text mining approaches as well as data description, linking and harmonization in the context of COVID-19, we have developed an ontology representing major novel coronavirus (SARS-CoV-2) entities. The ontology has a strong scope on chemical entities suited for drug repurposing, as this is a major target of ongoing COVID-19 therapeutic development.

RESULTS

The ontology comprises 2270 classes of concepts and 38 987 axioms (2622 logical axioms and 2434 declaration axioms). It depicts the roles of molecular and cellular entities in virus-host interactions and in the virus life cycle, as well as a wide spectrum of medical and epidemiological concepts linked to COVID-19. The performance of the ontology has been tested on Medline and the COVID-19 corpus provided by the Allen Institute.

AVAILABILITYAND IMPLEMENTATION

COVID-19 Ontology is released under a Creative Commons 4.0 License and shared via https://github.com/covid-19-ontology/covid-19. The ontology is also deposited in BioPortal at https://bioportal.bioontology.org/ontologies/COVID-19.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

动机

COVID-19大流行促使学术界在全球范围内做出了令人瞩目的响应。为了支持在COVID-19背景下的文本挖掘方法以及数据描述、链接和协调，我们开发了一个表示主要新型冠状病毒（SARS-CoV-2）实体的本体。该本体在适用于药物重新利用的化学实体方面具有很强的范围，因为这是当前COVID-19治疗开发的一个主要目标。

结果

该本体包含2270个概念类和38987条公理（2622条逻辑公理和2434条声明公理）。它描述了分子和细胞实体在病毒-宿主相互作用以及病毒生命周期中的作用，以及与COVID-19相关的广泛医学和流行病学概念。该本体的性能已在Medline和艾伦研究所提供的COVID-19语料库上进行了测试。

可用性和实现方式

COVID-19本体根据知识共享4.0许可发布，并通过https://github.com/covid-19-ontology/covid-19共享。该本体也存放在BioPortal上，网址为https://bioportal.bioontology.org/ontologies/COVID-19。

补充信息

补充数据可在《生物信息学》在线获取。