TY - JOUR
T1 - Ontological modeling and analysis of experimentally or clinically verified drugs against coronavirus infection
AU - Liu, Yingtong
AU - Hur, Junguk
AU - Chan, Wallace K.B.
AU - Wang, Zhigang
AU - Xie, Jiangan
AU - Sun, Duxin
AU - Handelman, Samuel
AU - Sexton, Jonathan
AU - Yu, Hong
AU - He, Yongqun
N1 - Funding Information:
This work was supported by a Global Reach fund and a bridge fund to YH at the University of Michigan Medical School and the University of North Dakota Host-Pathogen Interactions COBRE Pilot grant to JH. YH has been supported by a grant from the Michigan Medicine – Peking University Health Sciences Center Joint Institute for Clinical and Translational Research. The research has also received funding from the National Natural Science Foundation of China (Grant Nos. 61801067), the Natural Science Foundation of Chongqing (Grant No. cstc2018jcyjAX0243), the non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences 2019PT320003 and the Guizhou Science and Technology Cooperation Support Project (Grant No. [2020]4Y002). The article-processing charge was paid by a discretionary fund from Dr. William King, the director of the Unit for Laboratory Animal Medicine (ULAM) in the University of Michigan. We acknowledge ChEBI team’s inclusion of our submitted Remdesivir record to ChEBI. An early version of this manuscript was released as a preprint at https://www.preprints.org/manuscript/202003.0413/v154. Note that this version has many significant changes compared to the preprint version.
PY - 2021/12
Y1 - 2021/12
N2 - Our systematic literature collection and annotation identified 106 chemical drugs and 31 antibodies effective against the infection of at least one human coronavirus (including SARS-CoV, SAR-CoV-2, and MERS-CoV) in vitro or in vivo in an experimental or clinical setting. A total of 163 drug protein targets were identified, and 125 biological processes involving the drug targets were significantly enriched based on a Gene Ontology (GO) enrichment analysis. The Coronavirus Infectious Disease Ontology (CIDO) was used as an ontological platform to represent the anti-coronaviral drugs, chemical compounds, drug targets, biological processes, viruses, and the relations among these entities. In addition to new term generation, CIDO also adopted various terms from existing ontologies and developed new relations and axioms to semantically represent our annotated knowledge. The CIDO knowledgebase was systematically analyzed for scientific insights. To support rational drug design, a “Host-coronavirus interaction (HCI) checkpoint cocktail” strategy was proposed to interrupt the important checkpoints in the dynamic HCI network, and ontologies would greatly support the design process with interoperable knowledge representation and reasoning.
AB - Our systematic literature collection and annotation identified 106 chemical drugs and 31 antibodies effective against the infection of at least one human coronavirus (including SARS-CoV, SAR-CoV-2, and MERS-CoV) in vitro or in vivo in an experimental or clinical setting. A total of 163 drug protein targets were identified, and 125 biological processes involving the drug targets were significantly enriched based on a Gene Ontology (GO) enrichment analysis. The Coronavirus Infectious Disease Ontology (CIDO) was used as an ontological platform to represent the anti-coronaviral drugs, chemical compounds, drug targets, biological processes, viruses, and the relations among these entities. In addition to new term generation, CIDO also adopted various terms from existing ontologies and developed new relations and axioms to semantically represent our annotated knowledge. The CIDO knowledgebase was systematically analyzed for scientific insights. To support rational drug design, a “Host-coronavirus interaction (HCI) checkpoint cocktail” strategy was proposed to interrupt the important checkpoints in the dynamic HCI network, and ontologies would greatly support the design process with interoperable knowledge representation and reasoning.
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U2 - 10.1038/s41597-021-00799-w
DO - 10.1038/s41597-021-00799-w
M3 - Article
C2 - 33441564
AN - SCOPUS:85099354652
SN - 2052-4463
VL - 8
JO - Scientific data
JF - Scientific data
IS - 1
M1 - 16
ER -