ISMB 2022 Meeting


Bio-Ontologies ( is an International Society of Molecular Biology (ISMB) Community of Special Interest (COSI) and working group focused on the FAIR development and application of ontologies and other Linked Open Data resources, the latest and most innovative research in the application of these data, and the organization, presentation, and dissemination of knowledge in biomedicine and the life sciences.

Bio-Ontologies was in its 25th year at ISMB 2022 (, which was held in-person and online between July 10-14, 2022 and featured two days of exciting keynotes and cutting-edge research.

2022 Keynote Speakers

Encoding Biases’ Influences on Development and Use of Ontologies in the Life Sciences

Maria Keet, University of Cape Town


Ontology authoring, sometimes referred to as the ‘implementation’ stage of representing the knowledge, may seem like a just-do-it task, but even when experts agree on what to represent, there are a myriad of ways how to represent it. Consistently adhered to, they lead to transformable modelling styles. Different representation choices may clash with other ontologies to reuse, however, and with some of the purposes that an ontology may have been built for. Cognizance of such differences may facilitate smoother deployment of ontologies in applications with different requirements. They also pose challenges on methods and tools, such as for competency questions and verification with them, test-driven development, and various bottom-up ontology development approaches, such as knowledge extraction from biological diagrams. In this talk we take a tour through new insights into such factors that slow down or speed up development of bio-ontologies and their use in tools for the life sciences.


C. Maria Keet (PhD, MSc, MA, BSc(hons)) is an Associate Professor with the Department of Computer Science, University of Cape Town. She focuses on ontology engineering, conceptual data modelling, and their interaction with natural language, and bio-ontologies intermittently, which has resulted in some 150 peer-reviewed publications. She is PI on an NRF-funded project on NLG for Nguni languages, and was PI on an DST/MINCyT-funded project on ontology-driven conceptual modelling, and was involved in several EU projects. She coordinated the development of several tools and has written the first textbook on ontology engineering for computer scientists. She has served on many conference and workshop program committees and reviewed for numerous journals; recently she was PC (co-)chair of the IJCAI 2021 Demo track and EKAW 2020, and is for the ISWC 2022 resources track. Before her employment at UCT, Maria has worked at the University of KwaZulu-Natal, South Africa, and the KRDB Research Centre, Free University of Bozen-Bolzano, Italy where she also obtained a PhD in Computer Science in 2008. She also holds a BSc(honours) 1st class in IT & Computing from the Open University UK (2004), an MSc in Food Science (Microbiology) from Wageningen University, the Netherlands (1998), and an MA 1st class in Peace & Development Studies from the University of Limerick, Ireland (2003).

The Open Data Highway: Turbo-Boosting Translational Traffic with Ontologies

Melissa Haendel, University of Colorado Anschutz Medical Campus

Keynote shared with BOSC


Melissa Haendel is the Chief Research Informatics Officer and Marsico Chair in Data Science at University of Colorado Anschutz Medical Campus, and the Director of the Center for Data to Health (CD2H). Her background is molecular genetics and developmental biology as well as translational informatics, with a focus over the past decade on open science and semantic engineering. Dr. Haendel’s vision is to weave together healthcare systems, basic science research, and patient-generated data through development of data-integration technologies and innovative data capture strategies. Dr. Haendel’s research has focused on integration of genotype-phenotype data to improve rare-disease diagnosis and mechanism discovery. She also leads and participates in international standards organizations to support improved data sharing and utility worldwide.

Submission Information

Submission Types

We invite the submissions of proceedings papers (9 pages), short papers (2 pages), flash updates (1-2 pages), and poster abstracts (1 page). All relevant topics are invited. Please note that all page limits include references/works cited.

Example topics include (but not limited to):

  • Ontologies for infectious disease monitoring and prediction

  • Ontologies for climate change and its impact on human health

  • Ontologies in annotations, mapping applications, and metadata standards

  • FAIR data systems and application of ontologies and other Linked Open Data

  • Bio-curation platforms, collaborative ontology authoring

  • Ontology evolution, quality, and evaluation

  • Ontologies, knowledge representation, and reasoning

  • Machine (deep) learning and ontologies

  • Text mining and ontologies

  • Semantic Web-enabled applications

  • Ontologies for biomedical research, health informatics, and health care

  • Flash Updates on new and/or existing ontologies, Linked Open Data resources, tools, and applications

  • Descriptions of DevOps and other types of technical infrastructure and pipelines

New this year, we invite Early Career Submissions as lightning talks (1-2 pages). These submissions are intended to provide graduate students with the opportunity to present a short description of their research project at one of the leading conferences in computational biology and get first-hand feedback and mentorship from senior researchers in their field. This submission is open to Masters and Doctoral students who have not defended their thesis before the submission deadline.

Submission Instructions

Submissions can be made on the ISMB site ( For proceedings, please follow the instructions provided on the ISMB site. For all other submissions, please prepare your submission using the templates on the Bio-Ontologies website (

All submissions are reviewed (review criteria provided below). Following review, successful short papers (20 minutes), flash updates (5 minutes), and early career (5 minutes) submissions will be presented at the Bio-Ontologies COSI. Unsuccessful paper submissions will automatically be considered for flash updates presentations. All submissions will be considered for poster presentations.

Accepted submissions require that one author register for the conference and present the work. The presenter should identify themselves as the corresponding author during the submission process. All accepted submissions will be cataloged in the 2022 Bio-Ontologies Zenodo Community and provided with a citable DOI. Accepted submissions will also be invited to publish an extended version of their work in the Bio-Ontologies Thematic Series through the Journal of Biomedical Semantics.

Submission Review Criteria

All submissions to Bio-Ontologies are reviewed. Review criteria include:

  • Relevance of the topic to conference attendees.

  • Significance of the problem, such that reviewers understand that it is a problem that is important and worth solving.

  • Novelty of the approach, including critical discussion of related work.

  • Soundness and potential for reproducibility of the study and/or methods.

  • Quality of writing, including readability and clearly stated contribution(s).

Important Dates


  • Monday, November 29, 2021: Call for Proceedings Opens

  • Thursday, January 13, 2022 (11:59 PM any timezone): Submission Deadline

  • Thursday, March 3, 2022: Conditional Acceptance Notification

  • Thursday, March 17, 2022: Revised Papers Deadline

  • Monday, April 4, 2022: Final Acceptance Notification

Short Papers, Flash Updates, Early Career, and Poster Abstracts

  • Monday, January 24, 2022: Call for Abstracts Opens

  • Thursday, April 21, 2022 (11:59 PM EDT): Abstract Submission Deadline

  • Monday, April 25, 2022: Late Poster Submissions Open

  • Thursday, May 12, 2022: Talk and/or Poster Acceptance Notifications

  • Thursday, May 19, 2022 (11:59 PM EDT): Late Poster Submissions Deadline

  • Thursday, May 26, 2022: Late Posters Acceptance Notifications

Submission Templates

For proceedings, please follow the instructions provided on the ISMB site. For all other submissions, please prepare your submission using the templates on the Bio-Ontologies website (

Accessing Bio-Ontologies Templates (using the links below)

For Bio-Ontologies templates, please click on the link below matching your submission of choice. This will open up a new Google Docs window. From there, go to "File" --> "Download" and select your file type. A screenshot demonstrating this behavior is shown to the right.

For Proceedings Submissions

To find the Bio-Ontologies COSI when making your submission, please select "Biomedical Informatics" as the Track.

Poster Abstract Flash Updates


Short Papers


Early Career Submissions


2022 Bio-Ontologies Committees

Organizing Committee

Núria Queralt Rosinach

Leiden University Medical Center

The Netherlands

  • Committee Representative

Maxat Kulmanov

King Abdullah University of Science and Technology

Saudi Arabia

  • Alternate Committee Representative

  • Nominated Area Chair

Tiffany Callahan

Columbia University

United States of America

  • Proceedings Liaison

  • Track Chair

Robert Hoehndorf

King Abdullah University of Science and Technology

Saudi Arabia

  • Alternate Proceedings Liaison

  • Alternate Track Chair

National Institutes of Health

United States of America

University of Michigan

United States of America

University of Colorado

Anschutz Medical Campus

United States of America

Program Committee

King Abdullah University of

Science and Technology

Saudi Arabia

Columbia University

United States of America

Leiden University Medical Center

The Netherlands

Maastricht University

The Netherlands


If you have any questions please feel free to send us an email (, direct message us on Slack (, or post a message on Twitter (@bioontologies) or our LinkedIn Group (

Previous ISMB Meetings

Bio-Ontologies has been running since 1998, please use the ISMB Annual Meeting drop-down menu above to access content from prior meetings.