COVID-19 Literature Knowledge Graph Construction and Drug Repurposing Report Generation

Qingyun Wang; Manling Li; Xuan Wang; Nikolaus Parulian; Guangxing Han; Jiawei Ma; Jingxuan Tu; Ying Lin; Haoran Zhang; Weili Liu; Aabhas Chauhan; Yingjun Guan; Bangzheng Li; Ruisong Li; Xiangchen Song; Yi R. Fung; Heng Ji; Jiawei Han; Shih-Fu Chang; James Pustejovsky; Jasmine Rah; David Liem; Ahmed Elsayed; Martha Palmer; Clare Voss; Cynthia Schneider; Boyan Onyshkevych

doi:10.18653/v1/2021.naacl-demos.8

COVID-19 Literature Knowledge Graph Construction and Drug Repurposing Report Generation

Qingyun Wang
, Manling Li
, Xuan Wang
, Nikolaus Parulian
, Guangxing Han
, Jiawei Ma
, Jingxuan Tu
, Ying Lin
, Haoran Zhang
, Weili Liu
, Aabhas Chauhan
, Yingjun Guan
, Bangzheng Li
, Ruisong Li
, Xiangchen Song
, Yi R. Fung
, Heng Ji
, Jiawei Han
, Shih-Fu Chang
, James Pustejovsky

Jasmine Rah, David Liem, Ahmed Elsayed, Martha Palmer, Clare Voss, Cynthia Schneider, Boyan Onyshkevych

Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review

51 Citations (Scopus)

11 Downloads (CityUHK Scholars)

Abstract

To combat COVID-19, both clinicians and scientists need to digest vast amounts of relevant biomedical knowledge in scientific literature to understand the disease mechanism and related biological functions. We have developed a novel and comprehensive knowledge discovery framework, COVID-KG to extract fine-grained multimedia knowledge elements (entities and their visual chemical structures, relations and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures, and knowledge subgraphs as evidence. All of the data, KGs, reports, resources, and shared services are publicly available. © 2021 Association for Computational Linguistics.

Original language	English
Title of host publication	NAACL-HLT 2021 - The 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies
Subtitle of host publication	Demonstrations
Editors	Avi Sil, Xi Victoria Lin
Place of Publication	Stroudsburg, PA
Publisher	Association for Computational Linguistics
Pages	66-77
ISBN (Print)	9781954085480
DOIs	https://doi.org/10.18653/v1/2021.naacl-demos.8
Publication status	Published - Jun 2021
Externally published	Yes
Event	2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (NAACL-HLT 2021) - Virtual Duration: 6 Jun 2021 → 11 Jun 2021 https://2021.naacl.org/

Publication series

Name	NAACL-HLT - Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Demonstrations

Conference

Conference	2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (NAACL-HLT 2021)
Abbreviated title	NAACL 2021
Period	6/06/21 → 11/06/21
Internet address	https://2021.naacl.org/

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Publisher's Copyright Statement

This full text is made available under CC-BY 4.0. https://creativecommons.org/licenses/by/4.0/

Policy Impact

Cited in Policy Documents

Access Output

10.18653/v1/2021.naacl-demos.8

244893536.pdfFinal Published version, 2.13 MBLicence: CC BY

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Wang, Q., Li, M., Wang, X., Parulian, N., Han, G., Ma, J., Tu, J., Lin, Y., Zhang, H., Liu, W., Chauhan, A., Guan, Y., Li, B., Li, R., Song, X., Fung, Y. R., Ji, H., Han, J., Chang, S.-F., ... Onyshkevych, B. (2021). COVID-19 Literature Knowledge Graph Construction and Drug Repurposing Report Generation. In A. Sil, & X. V. Lin (Eds.), NAACL-HLT 2021 - The 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies: Demonstrations (pp. 66-77). (NAACL-HLT - Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Demonstrations). Association for Computational Linguistics. https://doi.org/10.18653/v1/2021.naacl-demos.8

Wang, Qingyun ; Li, Manling ; Wang, Xuan et al. / COVID-19 Literature Knowledge Graph Construction and Drug Repurposing Report Generation. NAACL-HLT 2021 - The 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies: Demonstrations. editor / Avi Sil ; Xi Victoria Lin. Stroudsburg, PA : Association for Computational Linguistics, 2021. pp. 66-77 (NAACL-HLT - Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Demonstrations).

@inproceedings{4dd27e8982cb406a9e7587ec4a05d64c,

title = "COVID-19 Literature Knowledge Graph Construction and Drug Repurposing Report Generation",

abstract = "To combat COVID-19, both clinicians and scientists need to digest vast amounts of relevant biomedical knowledge in scientific literature to understand the disease mechanism and related biological functions. We have developed a novel and comprehensive knowledge discovery framework, COVID-KG to extract fine-grained multimedia knowledge elements (entities and their visual chemical structures, relations and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures, and knowledge subgraphs as evidence. All of the data, KGs, reports, resources, and shared services are publicly available. {\textcopyright} 2021 Association for Computational Linguistics.",

author = "Qingyun Wang and Manling Li and Xuan Wang and Nikolaus Parulian and Guangxing Han and Jiawei Ma and Jingxuan Tu and Ying Lin and Haoran Zhang and Weili Liu and Aabhas Chauhan and Yingjun Guan and Bangzheng Li and Ruisong Li and Xiangchen Song and Fung, \{Yi R.\} and Heng Ji and Jiawei Han and Shih-Fu Chang and James Pustejovsky and Jasmine Rah and David Liem and Ahmed Elsayed and Martha Palmer and Clare Voss and Cynthia Schneider and Boyan Onyshkevych",

year = "2021",

month = jun,

doi = "10.18653/v1/2021.naacl-demos.8",

language = "English",

isbn = "9781954085480",

series = "NAACL-HLT - Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Demonstrations",

publisher = "Association for Computational Linguistics",

pages = "66--77",

editor = "Avi Sil and Lin, \{Xi Victoria\}",

booktitle = "NAACL-HLT 2021 - The 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies",

address = "United States",

note = "2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (NAACL-HLT 2021), NAACL 2021 ; Conference date: 06-06-2021 Through 11-06-2021",

url = "https://2021.naacl.org/",

}

Wang, Q, Li, M, Wang, X, Parulian, N, Han, G, Ma, J, Tu, J, Lin, Y, Zhang, H, Liu, W, Chauhan, A, Guan, Y, Li, B, Li, R, Song, X, Fung, YR, Ji, H, Han, J, Chang, S-F, Pustejovsky, J, Rah, J, Liem, D, Elsayed, A, Palmer, M, Voss, C, Schneider, C & Onyshkevych, B 2021, COVID-19 Literature Knowledge Graph Construction and Drug Repurposing Report Generation. in A Sil & XV Lin (eds), NAACL-HLT 2021 - The 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies: Demonstrations. NAACL-HLT - Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Demonstrations, Association for Computational Linguistics, Stroudsburg, PA, pp. 66-77, 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (NAACL-HLT 2021), 6/06/21. https://doi.org/10.18653/v1/2021.naacl-demos.8

COVID-19 Literature Knowledge Graph Construction and Drug Repurposing Report Generation. / Wang, Qingyun; Li, Manling; Wang, Xuan et al.
NAACL-HLT 2021 - The 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies: Demonstrations. ed. / Avi Sil; Xi Victoria Lin. Stroudsburg, PA: Association for Computational Linguistics, 2021. p. 66-77 (NAACL-HLT - Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Demonstrations).

Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review

TY - GEN

T1 - COVID-19 Literature Knowledge Graph Construction and Drug Repurposing Report Generation

AU - Wang, Qingyun

AU - Li, Manling

AU - Wang, Xuan

AU - Parulian, Nikolaus

AU - Han, Guangxing

AU - Ma, Jiawei

AU - Tu, Jingxuan

AU - Lin, Ying

AU - Zhang, Haoran

AU - Liu, Weili

AU - Chauhan, Aabhas

AU - Guan, Yingjun

AU - Li, Bangzheng

AU - Li, Ruisong

AU - Song, Xiangchen

AU - Fung, Yi R.

AU - Ji, Heng

AU - Han, Jiawei

AU - Chang, Shih-Fu

AU - Pustejovsky, James

AU - Rah, Jasmine

AU - Liem, David

AU - Elsayed, Ahmed

AU - Palmer, Martha

AU - Voss, Clare

AU - Schneider, Cynthia

AU - Onyshkevych, Boyan

PY - 2021/6

Y1 - 2021/6

N2 - To combat COVID-19, both clinicians and scientists need to digest vast amounts of relevant biomedical knowledge in scientific literature to understand the disease mechanism and related biological functions. We have developed a novel and comprehensive knowledge discovery framework, COVID-KG to extract fine-grained multimedia knowledge elements (entities and their visual chemical structures, relations and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures, and knowledge subgraphs as evidence. All of the data, KGs, reports, resources, and shared services are publicly available. © 2021 Association for Computational Linguistics.

AB - To combat COVID-19, both clinicians and scientists need to digest vast amounts of relevant biomedical knowledge in scientific literature to understand the disease mechanism and related biological functions. We have developed a novel and comprehensive knowledge discovery framework, COVID-KG to extract fine-grained multimedia knowledge elements (entities and their visual chemical structures, relations and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures, and knowledge subgraphs as evidence. All of the data, KGs, reports, resources, and shared services are publicly available. © 2021 Association for Computational Linguistics.

UR - https://www.scopus.com/pages/publications/85122303251

UR - https://www.scopus.com/record/pubmetrics.uri?eid=2-s2.0-85122303251&origin=recordpage

UR - https://app-overton-io.ezproxy.cityu.edu.hk/articles.php?query=10.18653/v1/2021.naacl-demos.8

U2 - 10.18653/v1/2021.naacl-demos.8

DO - 10.18653/v1/2021.naacl-demos.8

M3 - RGC 32 - Refereed conference paper (with host publication)

SN - 9781954085480

T3 - NAACL-HLT - Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Demonstrations

SP - 66

EP - 77

BT - NAACL-HLT 2021 - The 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies

A2 - Sil, Avi

A2 - Lin, Xi Victoria

PB - Association for Computational Linguistics

CY - Stroudsburg, PA

T2 - 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (NAACL-HLT 2021)

Y2 - 6 June 2021 through 11 June 2021

ER -

Wang Q, Li M, Wang X, Parulian N, Han G, Ma J et al. COVID-19 Literature Knowledge Graph Construction and Drug Repurposing Report Generation. In Sil A, Lin XV, editors, NAACL-HLT 2021 - The 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies: Demonstrations. Stroudsburg, PA: Association for Computational Linguistics. 2021. p. 66-77. (NAACL-HLT - Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Demonstrations). doi: 10.18653/v1/2021.naacl-demos.8

COVID-19 Literature Knowledge Graph Construction and Drug Repurposing Report Generation

Abstract

Publication series

Conference

UN SDGs

Publisher's Copyright Statement

Policy Impact

Access Output

Other Access Options

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