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WSBO-2021: Workshop on Synergizing Biomedical Ontologies

July 14-16, 2021 (Virtual)


Ontologies are standardized, formal vocabularies developed by domain experts, typically in collaboration with ontologists. In the era of big data and AI, they enable finding, accessing, interoperating and reusing datasets and other digital research objects, in other words, making data F.A.I.R. As more communities develop ontologies to meet their specific needs, it is critical that we maintain synergy with existing ontologies, especially reference ontologies. Similar, but unreferenced terms create ambiguities that complicate implementation of the very F.A.I.R. principles ontologies seek to support. The biomedical field is especially rich with similar ontologies, including BAO and OBI, MONDO and DOID, DTO and PR, CLO and BRENDA, UBERON and FMA, and others. Extensive mapping efforts are often required to maintain associations between these ontologies, making integration expensive and cumbersome. No formal process has been established for collaboratively converging and actively maintaining synergy between ontologies. The goal of this meeting is to stimulate conversation around the best practices for synergizing ontologies, with an emphasis on collaborative development and dynamic workflows.

Presentation Recordings now available!

Public Google Doc for Questions & Followup Discussion:

Finalized Program Schedule

Abstracts are now available in our downloadable Workshop Booklet:

Day 1: Wednesday, July 14, 2021. 8:00 am EDT - 12:00 pm EDT

8:00-8:20 am EDT: Welcome & Opening Remarks with Stephan Schürer [slides, recording]

8:20-8:40 am EDT: Martin Romacker. Synergizing Biomedical Ontologies – An Industry Perspective [slides, recording]

8:40-9:00 am EDT: David Osumi-Sutherland, Nicolas Matentzoglu, James McLaughlin, Henriette Harmse, Susan Bello, Nicole Vasilevsky, James Balhoff, Christopher Mungall, Melissa Haendel and Helen Parkinson. Ontology mappings - untangling the hairball and democratising the results [recording]

9:00-9:20 am EDT: Ernesto Jimenez-Ruiz, Thomas Liener and Ian Harrow. Matching life sciences ontologies in the Ontology Alignment Evaluation Initiative. [slides, recording]

9:20-9:40 am EDT: Lynn Schriml. FAIRifying biomedical ontology synergy. [slides, recording]

Break: 20 minutes

10:00-10:40 am EDT: Keynote Presentation, Melissa Haendel, The dangers of bad mappings: How imprecise and incomplete mappings can cost lives! [slides, recording]

10:40-11:00 am EDT: Darren Natale. Towards automating the ontological representation of proteins in the Protein Ontology. [recording]

11:00-11:20 am EDT: Nicolas Matentzoglu. A Simple Standard for Sharing Ontology Mappings (SSSOM). [slides,recording]

11:20-11:50 am EDT: Breakout Session. Stephan Schürer. Needs for synergization in the biomedical ontology community.

Day 2: Thursday, July 15, 2021. 12:00 pm ET - 4:10 pm ET

12:00-12:20 pm EDT: Opening Remarks with Mark Musen [recording]

12:20-1:00 pm EDT: Keynote Presentation, Lucila Ohno-Machado, FAIRness and fairness in sharing data from study participants and patients [recording]

1:00-1:20 pm EDT: Susan Bello, Nicole Vasilevsky, Nicolas Matentzoglu, David Osumi-Sutherland and The Upheno Team. Bridging the Phenotype Divide by Using Shared Patterns. [slides, recording]

1:20-1:40 pm EDT: Christopher Mungall. Synergizing Biomedical Ontologies with Genomics Databases. [slides, recording]

1:40-2:00 pm EDT: John Turner. OntoloBridge: Connecting Ontology Users and Ontology Maintainers! [recording]

Break: 20 minutes

2:20-2:40 pm EDT: James Balhoff and Christopher Mungall. Resolving ontology mappings using Boomer. [slides, recording]

2:40-3:00 pm EDT: Oliver He. Development and maintenance of the interoperable and synergistic Cell Line Ontology [recording]

3:00-3:20 pm EDT: Asiyah Lin, Alex Welsch and Lawrence Callahan. What End Users Need from the Ontology Community? - Experience from NCPI, FDA, and COVID-19 Ontologies Harmonization effort. [slides, recording]

3:20-3:40 pm EDT: Samantha Jeschonek. CDD Annotator and Perspectives from the Data FAIRy Initiative [recording]

3:40-4:10 pm EDT: Breakout Session. Asiyah Lin. Integrating online ontology tools.

Day 3: Friday, July 16, 2021. 11:00 am EDT - 1:00 pm EDT

11:00-11:10 am EDT: Opening Remarks with Hande Kucuk McGinty. [recording]

11:10-11:25 am EDT: Rebecca Jackson. Automating Ontology Mapping Workflows With ROBOT [slides, recording]

11:25-11:30 am EDT: Kai Blumberg. Harmonizing Units of Measure Vocabularies on the Web: a Basic Prototype [slides, recording]

11:30-11:40 am EDT: Hande Kucuk McGinty. Thinking about the Future: Ontologies for Whole-Person and Holistic-Healthcare Research [recording]

11:40-11:50 am EDT: Damion Dooley. OBO Foundry Domain Coverage for Food, One Health, and Holistic Healthcare [recording]

11:50-12:20 pm EDT: Sheryl Denker and Antal Berenyi. Describing the Need: An Ontology End-User Case Study [recording]

12:20-12:30 pm EDT: Whitney Smith. Collaborative Drug Discovery – Supporting the Future of FAIR Data Management [recording]

12:30-12:45 pm EDT: Closing Remarks with Stephan Schürer and Mark Musen [recording]

12:45-1:00 pm EDT: (Optional) Conference Feedback

Venue: Online (Zoom)

Join Zoom Meeting

Meeting ID: 857 4331 0822 Passcode: 822481

Submissions (CLOSED)

We welcome submissions of abstracts of 300 words or less for oral presentations and tool demos. Submit your abstract here:

Selected abstracts will give a presentation not to exceed 15 minutes plus an additional 5 minutes for audience questions (for a total of 20 minutes).

Presentations may fall into any of the following categories

  • Developing and maintaining biomedical ontologies
  • End-user interaction with ontologies
  • Ontology mapping
  • Tools, technologies, and repositories supporting ontologies
  • Ontology software or web ecosystems (e.g.: BioPortal, Protege, OntoAnimal)


Workshop Co-organizers:

  • Samantha Jeschonek (Collaborative Drug Discovery)
  • Asiyah Yu Lin (National Institutes of Health)
  • Hande Kucuk McGinty (Ohio University)

Workshop Co-chairs

  • Stephan Schürer (University of Miami)
  • Mark Musen (Stanford University)


Workshop on Synergizing Biomedical Ontologies, July 14-16 (Virtual)



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