CIDO: Coronavirus Infectious Disease Ontology
The emerging COVID-19 outbreak has reminded everyone the early versions of the SARS coronavirus outbreak and the Middle East coronavirus outbreak. These coronavirus outbreaks have made us realize the critical importance of systematically studying these coronavirus infectious diseases using the cutting edge technologies. Ontology provides a unique angle to study the coronavirus infectious diseases.
The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment. Its development follows the OBO Foundry Principles.
CIDO has now been approved to be an OBO library ontology: http://obofoundry.org/ontology/cido.html.
CIDO was initiated and co-led by Dr. Hong Yu, director of Department of Respiratory and critical Care Medicine，Guizhou Province People’s Hospital, Guizhou University Medical College, Guiyang, Guizhou, China, and Dr. Yongqun Oliver He, Associate Professor, University of Michigan Medical School, Ann Arbor, MI, USA.
He laboratory at the University of Michigan actively participated in the CIDO development. In addition to Oliver He, four graduate students (Anthony Huffman, Yingtong Liu, Edison Ong, and Yang Wang), and several undergraduate students (including Easheta Shah, Roshan Desai) have actively involved in the CIDO development.
Drs. Hong Yu and Yang Wang from Guizhou Province People’s Hospital have also participated in the CIDO development. Dr. Yang Wang (M.D.) is also a PhD student in Biomedical Informatics and she is currently a visiting PhD student in He laboratory.
Many researchers in the University of Michigan, including Dr. Brian Athey and Dr. Gil Omenn, have participated in the CIDO development.
Dr. Junguk Hur from University of North Dakoda Medical School is also a CIDO developer. Dr. Hur is also interested in applying CIDO for more efficient literature mining.
Dr. Barry Smith, a well-known ontologist from the University at Buffalo, is also a member of our CIDO development team. Dr. Smith developed the Basic Formal Ontology (BFO), a top level ontology used by over 300 ontologies around the world. BFO has now been approved to become ISO/IEC standard 21838. CIDO is aligned with BFO, and by doing so, CIDO is aligned with the other hundreds of ontologies.
John Beverley, an expert in the area where ontology and logic meet, has been working on developing the modeling of viral infectious diseases as an extension of the core of Infectious Disease Ontology (IDO). John has joined our CIDO development.
Dr. Asiyah Yu Lin, M.D., Ph.D., an Health Scientist at FDA and an ontology expert. Asiyah is an affiliated ontologist in the National Center for Ontology Research.
Dr. Xiaolin Yang, an experienced ontologist and bioinformatician from the Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China, has also participated in our collaborative CIDO development and applications.
Dr. Bill Duncan, Software Developer at Lawrence Berkeley National Laboratory, Buffalo, New York.
Dr. Sivaram Arabandi, MD, MS., a clinical informatician and founder of ONTOPRO LLC with over 15 years of multidisciplinary clinical and information technology experience.
Dr. Liwei Wang and Dr. Hongfang Liu, medical informatics experts from Mayo Clinic who are using CIDO to support OHNLP clinical COVID-19 NLP research.
Dr. Suyuan Peng and Dr. Luxia Zhang from the Peking University have actively participated in this project, with the specific useage of ontology modeling, annotation, and analysis of the association between acute kidney injury (AKI) and COVID-19. This collaboration has been supported by a grant to Drs. Luxia Zhang and Oliver He from the Michigan Medicine–Peking University Health Sciences Center Joint Institute for Clinical and Translational Research (71017Y2027 and U072807),
More collaborators are provided below.
Everyone who would like to contribute to the CIDO development is welcome to join our development team. Thanks.
OWL format: https://raw.githubusercontent.com/CIDO-ontology/cido/master/src/ontology/cido.owl
https://github.com/CIDO-ontology/cido/issues
cido-discuss@googlegroups.com
http://obofoundry.org/ontology/cido.html.
He Y, Yu H, Ong E, Wang Y, Liu Y, Huffman A, Huang H, Beverley J, Hur J, Yang X, Chen L, Omenn GS, Athey B, Smith B. CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis. Scientific Data. (2020) 7:181 | https://doi.org/10.1038/s41597-020-0523-6. PMID: 32533075. PMCID: PMC7293349.
Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng, Anna Maria Masci, Liwei Wang, Hongfang Liu, Fatima Zohra Smaili, Robert Hoehndorf, Zoë May Pendlington, Paola Roncaglia, Xianwei Ye, Jiangan Xie, Yi-Wei Tang, Xiaolin Yang, Suyuan Peng, Luxia Zhang, Luonan Chen, Junguk Hur, Gilbert S. Omenn, Brian Athey, Barry Smith. ]A Comprehensive Update on CIDO: The Community-based Coronavirus Infectious Disease Ontology](https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-022-00279-z). Journal of Biomedical Semantics. 13, Article number: 25 (2022). https://doi.org/10.1186/s13326-022-00279-z. PMID: 36271389. PMCID: PMC9585694.