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.
Many graduate students, clinical doctors, and researchers in the He laboratory and Guizhou Province People’s Hospital have also participated in the CIDO development.
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.
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.
More collaborators are provided below.
Everyone who would like to contribute to the CIDO development is welcome to join our development team. Thanks.
- OBO Foundry ontologies, including Infectious Disease Ontology (IDO), Disease Ontology (DOID), Protein Ontology (PRO), Vaccine Ontology (VO), etc.
- CORD-19-on-FHIR -- Semantics for COVID-19 Discovery
- COVID-19 Biohackathon April 5-11 2020: https://github.com/virtual-biohackathons/covid-19-bh20
CIDO Source Link (Open licence: CC-BY 4.0):
OWL format: https://raw.githubusercontent.com/CIDO-ontology/cido/master/src/ontology/cido.owl
https://github.com/CIDO-ontology/cido/issues
http://obofoundry.org/ontology/cido.html.
- Ontobee: http://www.ontobee.org/ontology/CIDO
- BioPortal: http://bioportal.bioontology.org/ontologies/CIDO
- Liu Y, Chan W, Wang Z, Hur J, Xie J, Yu H, He Y. Ontological and bioinformatic analysis of anti-coronavirus drugs and their Implication for drug repurposing against COVID-19. Preprints. 2020, 2020030413 (doi: https://doi.org/10.20944/preprints202003.0413.v1). URL: https://www.preprints.org/manuscript/202003.0413/v1
- Ong E, Wong M, Huffman A, He Y. COVID-19 coronavirus vaccine design using reverse vaccinology and machine learning. bioRxiv. Posted on March 23, 2020. doi: https://doi.org/10.1101/2020.03.20.000141. URL: https://www.biorxiv.org/content/10.1101/2020.03.20.000141v2
- 3/12/2020: CIDO was approved and added to the OBO Foundry ontology library: http://obofoundry.org/ontology/cido.html.
- 3/12/2020: Oliver transferred the CIDO github organization location from github.com/biomedontology to the newly generated https://github.com/CIDO-ontology organization. Such a transfer is to better support its organization with more options (such as generating new repositories).
- 3/12/2020: Oliver generated the new CIDO-ontology github organization.
- 2/3/2020: Oliver submitted a request for the CIDO namespace in OBO-discuss email. See the email and discussions in OBO community here: https://groups.google.com/forum/#!topic/obo-discuss/AAZnGWe5eEE
- 1/26/2020: CIDO was submitted to Ontobee and BioPortal.
- 1/25/2020: The CIDO GitHub website was generated, and CIDO source was submitted to the GitHub website.
- 1/24/2020: The first version of CIDO was initiated by Oliver He and Hong Yu.