Bio-Ontologies (#bioontologies is an ISMB Community of Special Interest (COSI) that covers the latest and most innovative research in the application of ontologies and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. Join our mailing list and our slack team!  Have something to say? Tweet to @bioontologies or send an email to the organizers - .

Bio-Ontologies will be in its 22nd year at ISMB/ECCB 2019, which will be held in Basel, Switzerland between July 21-25. Bio-ontologies strives to provide a vibrant environment for reporting novel methods and sharing experiences on the construction and application of ontologies in health care and the life sciences. The COSI offers a constructive environment to nurture discussion of innovative and scientifically sound work that range from preliminary to completed, from both young and experienced investigators alike. Bio-Ontologies participants also benefit from a strongly interdisciplinary setting, where ISMB attendees intermingle with members from American Medical Informatics Association (AMIA) and the W3C’s Healthcare and Life Sciences Community Group (HCLSCG), thereby increasing impact through broader dissemination and enabling new and exceptional collaborations. This year's event will be integrated into the main conference and will feature papers accepted for the ISMB proceedings.

Selected papers will be invited to submit an extended version of their manuscript to the bio-ontologies theme in the Journal of Biomedical Semantics.

Key Dates

 Submission Deadline April 4, 2019 (for posters and talks)
 Late Poster Deadline  April 30, 2019
 Acceptance Notification May 2, 2019
 Late Poster Notification     May 21, 2019
 Program Information June 15, 2019
 Early Bird Registration June 20, 2019
 Bio-Ontologies track @ ISMB July 22-23, 2019
 Special Issue deadline October 1, 2019

Keynotes: TBD

Call for Submissions

We invite the submission of short papers, flash updates and posters for presentation at the Bio-Ontologies. Papers are invited in the following three areas:

1. The development of biological and biomedical ontologies to represent and structure knowledge.

2. Ontology-focused tools and methods (e.g. ontology engineering, ontology alignment, biocuration, information extraction, text mining, data integration) featuring biological use cases.

3. Biological applications of ontologies (e.g. ontologies use in data mining, machine learning, visualization, knowledge graphs, semantic query answering)

Deadlines and Presentation Length

We welcome short research papers (4 pages), flash updates (1 page) and poster abstracts (1 page) as a PDF using the Bio-ontologies template for papers ( or updates/posters ( Submissions can be made on the easychair site (not yet available). Please note that 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. The research presentations are normally allocated between 20 minutes while flash updates are presented in 5-10 minutes. 

Review Criteria

  1. Relevance, interest, and value of the topic to conference attendees.
  2. Significance of the problem, such that reviewers understand that it is a problem that is important and worth solving.
  3. Novelty of the approach, including critical discussion of related work.
  4. Soundness and potential for reproducibility of the study and/or methods.
  5. Quality of writing, including readability and clearly stated contribution(s)

Organizing Committee

Previous Meetings

Chicago (2018), Prague (2017), Orlando (2016), Dublin (2015), Boston (2014), Berlin (2013), Long Beach (2012), Vienna (2011), Boston (2010), Stockholm (2009), Toronto (2008), Vienna (2007), Fortaleza (2006), Detroit (2005), Glasgow (2004), Brisbane (2003), Edmonton (2002), Copenhagen (2001), San Diego (2000), Heidelberg (1999), Montreal (1998).


Have suggestions for this year? We'd love to hear from you at