CIDO: The community-based coronavirus infectious disease ontology

Yongqun He; Hong Yu; Edison Ong; Yang Wang; Yingtong Liu; Anthony Huffman; Hsin Hui Huang; John Beverley; Asiyah Yu Lin; William D. Duncan; Sivaram Arabandi; Jiangan Xie; Junguk Hur; Xiaolin Yang; Luonan Chen; Gilbert S. Omenn; Brian Athey; Barry Smith

CIDO: The community-based coronavirus infectious disease ontology

Yongqun He, Hong Yu, Edison Ong, Yang Wang, Yingtong Liu, Anthony Huffman, Hsin Hui Huang, John Beverley, Asiyah Yu Lin, William D. Duncan, Sivaram Arabandi, Jiangan Xie, Junguk Hur, Xiaolin Yang, Luonan Chen, Gilbert S. Omenn, Brian Athey, Barry Smith

Great Plains IDeA-CTR

Research output: Contribution to journal › Conference article › peer-review

2 Scopus citations

Abstract

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented.

Original language	English (US)
Journal	CEUR Workshop Proceedings
Volume	2807
State	Published - 2020
Event	11th International Conference on Biomedical Ontologies, ICBO 2020 - Joint with the 10th Workshop on Ontologies and Data in Life Sciences, ODLS 2020 and Part of the Bolzano Summer of Knowledge, BoSK 2020 - Virtual, Bolzano, Italy Duration: Sep 17 2020 → …

Keywords

COVID-19
Coronavirus
Drug repurposing
Ontology
Ventilator

ASJC Scopus subject areas

Computer Science(all)

Cite this

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title = "CIDO: The community-based coronavirus infectious disease ontology",

abstract = "Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented.",

keywords = "COVID-19, Coronavirus, Drug repurposing, Ontology, Ventilator",

author = "Yongqun He and Hong Yu and Edison Ong and Yang Wang and Yingtong Liu and Anthony Huffman and Huang, {Hsin Hui} and John Beverley and Lin, {Asiyah Yu} and Duncan, {William D.} and Sivaram Arabandi and Jiangan Xie and Junguk Hur and Xiaolin Yang and Luonan Chen and Omenn, {Gilbert S.} and Brian Athey and Barry Smith",

note = "Publisher Copyright: Copyright {\textcopyright} 2020 for this paper by its authors.; 11th International Conference on Biomedical Ontologies, ICBO 2020 - Joint with the 10th Workshop on Ontologies and Data in Life Sciences, ODLS 2020 and Part of the Bolzano Summer of Knowledge, BoSK 2020 ; Conference date: 17-09-2020",

year = "2020",

language = "English (US)",

volume = "2807",

journal = "CEUR Workshop Proceedings",

issn = "1613-0073",

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T1 - CIDO

T2 - 11th International Conference on Biomedical Ontologies, ICBO 2020 - Joint with the 10th Workshop on Ontologies and Data in Life Sciences, ODLS 2020 and Part of the Bolzano Summer of Knowledge, BoSK 2020

AU - He, Yongqun

AU - Yu, Hong

AU - Ong, Edison

AU - Wang, Yang

AU - Liu, Yingtong

AU - Huffman, Anthony

AU - Huang, Hsin Hui

AU - Beverley, John

AU - Lin, Asiyah Yu

AU - Duncan, William D.

AU - Arabandi, Sivaram

AU - Xie, Jiangan

AU - Hur, Junguk

AU - Yang, Xiaolin

AU - Chen, Luonan

AU - Omenn, Gilbert S.

AU - Athey, Brian

AU - Smith, Barry

PY - 2020

Y1 - 2020

N2 - Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented.

AB - Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented.

KW - COVID-19

KW - Coronavirus

KW - Drug repurposing

KW - Ontology

KW - Ventilator

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M3 - Conference article

AN - SCOPUS:85101058720

SN - 1613-0073

VL - 2807

JO - CEUR Workshop Proceedings

JF - CEUR Workshop Proceedings

Y2 - 17 September 2020

ER -

CIDO: The community-based coronavirus infectious disease ontology

Abstract

Keywords

ASJC Scopus subject areas

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