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WCO-2020: Workshop on COVID-19 Ontologies

8th Annual Workshop of the Clinical and Translational Science Ontology Group


COVID-19 is the first pandemic in the big data and AI era, and has resulted in unprecedented cooperation among global teams in the race to find cures. This has come with interesting data challenges, not just in the scale, but also in the variety of the data that is being generated and shared - data that is often generated using different models. Integration at this massive scale requires a coordinated effort by the clinical, research, government, informatics and other communities. This workshop on COVID-19 ontologies aims to bring together all the interested parties to share their experiences, ontologies, applications, lessons learned, and encourage more coordinated efforts to build effective models for semantic data integration and insights globally. The first Workshop on COVID-19 Ontologies (WCO-2020) is part of the CTSA Ontology Group meeting series. We invite everyone to join the WCO-2020!

This workshop will include the following themes:

  • Development of COVID-19 ontologies
  • Applications of ontologies, including:
    • User interface
    • Query and analysis
    • Visualization
    • Machine learning, AI, NLP
    • Demos of COVID-19 data usage and analysis (even if ontology is not used). The data can be clinical, research, social, economic, etc.

The talks from this workshop will be posted to the YouTube Channel Biomedical Ontology World

We are happy to announce our keynote speakers for the two sessions:

  • Dr. Warren Kibbe, Duke University. Topic: National COVID Cohort Collaborative (N3C) and mapping terminologies in a pandemic [video]
  • Dr. Gregory Pappas for late Dr. Michael Waters, Associate Director National Surveilence, Center for Biologics Evaluation and Research (CBER), FDA. Topic: SHIELD: Extracting Value from Daily Reported COVID-19 Test Data. (SHIELD )


Please register using the following Google form:

Program Schedule

One on ontology development, one on ontology applications

Day 1: 9:30 am - 2:30 pm ET, Friday, Oct 23 , 2020

This session will focus on the development aspect of COVID-19 related ontologies.

9:30-9:4O am ET: Open remarks

Session 1: Extending existing Ontologies for COVID-19 [Moderator: Sivaram]

  • 9:40-9:55 am ET: Yuki Yamagata, Tatsuya Kushida and Hiroshi Masuya. Knowledge systematization of COVID-19 infectious processes based on Homeostasis Imbalance Process (HoIP) Ontology [slides | video]
  • 9:55-10:10 am ET: Asiyah Lin, Philip Huang, Anthony Huffman and Yongqun He. Ontology-based representation and comparison of COVID-19 vaccine phase III clinical trials [slides | video]
  • 10:10-10:25 am ET: Leigh Carmody, Nico Matentzoglu, Lauren Chan, Nicole Vasilevsky, Hannah Blau, Michael Gargano and Peter Robinson. Medical Action Ontology (MAxO) expansion to include COVID19 treatment terms [slides | video]

Break: 5 min

Keynote 10:30-11:00 am ET: Dr. Warren Kibbe "National COVID Cohort Collaborative (N3C) and mapping terminologies in a pandemic" [video]

Break: 10 min

Session 2: Newly developed Ontologies specifically for COVID-19 [Moderator: Asiyah]

  • 11:10-11:25 am ET: Zoe May Pendlington, Paola Roncaglia, Nicolas Matentzoglu, David Osumi-Sutherland, Deborah Caucheteur, Julien Gobeill, Luc Mottin, Donat Agosti, Patrick Ruch and Helen Parkinson. COVoc: a COVID-19 ontology to support literature triage [slides | video]
  • 11:25-11:40 am ET: Luiz Olavo Bonino Da Silva Santos, Rajaram Kaliyaperumal, Marc Nieuwland, Jeroen Beliën, Bruna dos Santos Vieira and Lana Meiqari. A semantic data model for the WHO COVID-19 Case Report Form [slides | video]
  • 11:40-11:55 am ET: Biswanath Dutta and Michael DeBellis. CODO: An Ontology to Capture Data on the Covid-19 Pandemic [slides | video]
  • 11:55-12:10 pm ET: John Beverley, Shane Babcock and Barry Smith. Coordinating Coronavirus Research with IDO-COVID-19 [slides | video]
  • 12:10-12:25 pm ET: Yongqun He, Hong Yu, Edison Ong, Yang Wang, Yingtong Liu, Anthony Huffman, Hsin-Hui Huang, John Beverley, Asiyah Yu Lin, William Duncan, Sivaram Arabandi, Liwei Wang, Hongfang Liu, Yehoshua Perl, Jiangan Xie, Junguk Hur, Xiaolin Yang, Luonan Chen, Gilbert Omenn, Brian Athey and Barry Smith. CIDO: The Community-based Coronavirus Infectious Disease Ontology [slides | video]

Break: 5 min

Session 3: COVID-19 ontology resources [Moderator: Oliver]

  • 12:30-12:45 pm ET: Enrique Wulff. Covid-19 ontology resources for libraries [slides | video]
  • 12:45-1:00 pm ET: Victor Lee. Value Set-based Approach to Authoring Ontologies [slides | video]

Lunch Break (or free discussion): 30 min

Session 4: Group discussion

Collaborative COVID-19 metadata standardization to support timely publishing and tracking COVID 19 data, research and medical product trials for the greater good

Day 2: 9:30 am - 2:30 pm ET, Friday, Oct 30, 2020

This session will focus on the applications of COVID-19 related ontologies.

9:30-9:4O am ET: Open remarks

Session 1: Data standardization [Moderator: Oliver]

  • 9:40-9:55 am ET: Emma Griffiths, Ivan Gill, Damion Dooley, Rhiannon Cameron and William Hsiao. The DataHarmonizer: A fast, secure application for the harmonization of SARS-CoV-2 contextual data [video]
  • 9:55-10:10 am ET: Asiyah Lin, A.James Phillips, Aaron Glieberman, Mike Reed, Webb Stone, Sameer Rajesh, Veronique Baron, Faten Okda, Stephanie Ishack, Lellupitiyage Don Sujeewa Sampath, Kim Arvanites, Richard Creager,Tony Morrison, Marc L. Salit. Towards a Minimum Information Standard About a Viral Control (MIAViC) [video]

Keynote 10:10-10:40 am ET: Dr. Gregory Pappas for late Dr. Michael Waters Interoperability, Laboratory Data, And Real World Evidence (RWE): Where We Are? [video]

Break: 10 min

Session 2: Drug Analysis [Moderator: Asiyah]

  • 10:50-11:05 am ET: Zhichao Liu Artificial intelligence (AI). Powered drug repositioning for treating COVID-19 [video]
  • 11:05-11:20 am ET: Justin Reese, Deepak Unni, Tiffany Callahan, Luca Cappelletti, Vida Ravanmehr, Seth Carbon, Kent Shefchek, Tommaso Fontana, Hannah Blau, Nicolas Matentzoglu, Nomi Harris, Monica Munoz-Torres, Melissa Haendel, William Duncan, Nicole Vasilevsky, Peter Robinson, Marcin Joachimiak and Christopher Mungall. A knowledge graph for COVID-19 [video]
  • 11:20-11:35 am ET: Fatima Zohra Smaili, Yongqun He, Xin Gao and Robert Hoehndorf. Candidate COVID-19 Drugs Prediction [slides | video]

Break: 5 min

Session 3a: Knowledge and NLP [Moderator: Sivaram]

  • 11:40-11:55 am ET: Erico de Souza, Robert Warren, Daniel Buijs and Taehyun Kim. Dark Matter: A Health Canada Solution for Information Retrieval [video]
  • 11:55-12:10 pm ET: Brian Alper, Joanne Dehnbostel, Vignesh Subbian and Muhammad Afzal. Code System Development Protocol for Computable Expression of Scientific Knowledge [video]
  • 12:10-12:25 pm ET: Liwei Wang, Andrew Wen, Huan He, Sijia Liu, Yongqun He and Hongfang Liu. Standardizing COVID-19 clinical concepts for N3C analytics

Session 3b: Application tools [Moderator: Sivaram]

  • 12:25-12:40 am ET: John Turner, Caty Chung, Samantha Jeschonek, Hande Kucuk McGinty, Michael Dorf, John Graybeal and Stephan Schurer. OntoloBridge the FAIR-bridge between users of scientific vocabulary and ontology creators [video]
  • 12:40-12:55 am ET: Hande Küçük McGinty, Peter Gedeck, Samantha Jeschonek, Philip Cheung, Jason B. Harris, Barry Bunin and Alex Clark. Extending Machine Learning Capabilities of BioHarmony Annotator

Lunch Break (or free discussion): 30 min

Session 4: Group discussion [Moderator: Bill Hogan]

  • 1:25-2:30 pm ET: Discussion topics to be announced.

Venue: Online (Zoom virtual meeting)

We will send invites to those who have registered for the workshop.


We welcome submissions of abstracts of 300 words or less for oral presentations and tool demos. Images can be included, but limit the whole submission to one page. Please submit through the following Easychair website:


Workshop Co-organizers:

  • Asiyah Yu Lin (FDA, National Center for Ontological Research)
  • Bill Duncan (Lawrence Berkeley National Laboratory)
  • Sivaram Arabandi (Ontopro)
  • Yongqun “Oliver” He (University of Michigan Medical School)

CTSOG Co-chairs:

  • Bill Hogan (University of Florida College of Medicine, Gainesville, FL)
  • Barry Smith (University at Buffalo, Buffalo, NY)


  • CTSOG: Clinical and Translational Science Ontology Group.
  • MICHR: Michigan Institute for Clinical & Health Research (CTSA at Michigan).

Call for papers (closed):


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