ISMB/ECCB 2024 Meeting

About

Bio-Ontologies (http://www.bio-ontologies.org.uk/) 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 is in its 27th year at ISMB 2024 (https://www.iscb.org/ismb2024/home), which will be held in-person July 12-16, 2024 in Montreal, Canada and will feature two days of exciting keynotes and cutting-edge research.


2024 Keynote Speakers


Dr. Mayla R. Boguslav

Title: Learning from our collective scientific ignorance: How can ontologies help us determine what isn't yet?

Abstract:

Ontologies beg the question what is or exists (known knowns). I seek to determine what isn't or doesn't exist yet (known unknowns or questions). Ontologies aim to make knowledge accessible, transparent, and searchable. Biological ontologies define the entities and relations in biological domains. The community seeks to organize, present, and disseminate knowledge in biomedicine and the life sciences more generally. This can also be done for our collective scientific ignorance - our missing or incomplete knowledge. Let's make our collective scientific ignorance accessible, transparent, and searchable. In fact, research begins with a question and progresses by exploring new and uncharted territory. Enumerating what we don't know yet can help students, researchers, funders, and publishers generate novel research questions, prioritize resources, and rebuild trust in science. Further, ideally, we combine both knowledge and ignorance to determine solved and unsolved questions. I will present my ignorance taxonomy and ignorance-base (comparable to a knowledge-base) that used ontologies. More generally, I will present a new scientific method framework that shifts the focus to ignorance and questions, not just knowledge. Join me to talk about what we don’t know yet. 


Biography: 

Mayla R. Boguslav seeks to determine what isn't (yet). She works to uncover our collective scientific questions that are not yet answered by creating taxonomies and using ontologies. Focusing on what science has yet to answer helps researchers locate the role of their ongoing work, clarifies what scientists are saying and what they are not, and rebuilds trust in science. Mayla is a Postdoctoral Fellow in Mathematics at Colorado State University. She received the 2023 AMIA Edward H. Shortliffe Doctoral Dissertation Award for her PhD in Computational Biosciences from the University of Colorado Anschutz Medical Campus.

Dr. Karin Slater

Title: Exploring Multiple Perspectives for Associative Knowledgebases

Abstract: 

Databases encoding associative relationships between biomedical entities function as background knowledge that are leveraged for a range of purposes. For example, disease-phenotype associations are used for differential diagnosis and variant prediction, while gene-function associations are used in gene set enrichment analyses. 

In the ontology world, these associative knowledgebases lie somewhere between the conceptualisation and instance spaces, defining foundational knowledge that is often probabilistic, associative, or uncertain, rather than axiomatic. They are formed through some combination of manual curation from expert knowledge, experimental data, and analysis of co-occurrence in literature text. Due to this aetiology of associations, existing databases represent a particular perspective on biomedical knowledge, and it is one that differs from those that might be cultivated from analysis of other sources, such as clinical data, public discussion, or alternative modularisations of literature text. 

We will explore the similarities and differences between associative knowledgebases derived from these contexts, including methodological concerns, hypothesis generation, characterisation, and implications for downstream applications.


Biography: 

Dr. Slater is an Assistant Professor of Biomedical Semantics at the University of Birmingham, working in the Centre for Health Data Science and Centre for Environmental Research and Justice. With applications spanning healthcare, chemical risk assessment, and radiation biology, she is interested in multi-contextual representations of biomedical entities and developing practical methods for discerning actionable insights from data.


Submission Information


Submission Types

We invite the submissions of proceedings papers (9 pages), short papers (4 pages), flash updates (1-2 pages), and poster abstracts (1 page). We also 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. 


All relevant topics are invited. Example topics include (but not limited to):


Submission Instructions

Submissions can be made on the ISMB site (https://www.iscb.org/ismb2024/home). 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 (https://www.bio-ontologies.org.uk/2024-meeting).


All submissions are reviewed (review criteria provided on the Bio-Ontologies website). Following review, successful short papers (20 minutes), flash updates (5 minutes), and early career (5 minutes) submissions will be presented at either the Bio-Ontologies COSI, the BOSC COSI, or the joint Bio-Ontologies and BOSC COSI session. The selection of work to a specific COSI session is at the discretion of the Bio-Ontologies and BOSC joint organizing committee. 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 2024 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:

Important Dates

Proceedings

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

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 (https://www.bio-ontologies.org.uk/2024-meeting).


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

bio-ontologies-poster-or-flash-update-template

Short Papers

bio-ontologies-paper-template

Early Career Submissions

bio-ontologies-ecs-template

2024 Bio-Ontologies Committees


Organizing Committee

Núria Queralt Rosinach

Leiden University Medical Center

The Netherlands

Maxat Kulmanov

King Abdullah University of Science and Technology

Saudi Arabia

Tiffany Callahan

Columbia University

United States of America

Robert Hoehndorf

King Abdullah University of Science and Technology

Saudi Arabia


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

Maxat Kulmanov

King Abdullah University of Science and Technology Saudi Arabia

Questions?

If you have any questions please feel free to send us an email (bioontologies@gmail.com), direct message us on Slack (bioontologies.slack.com), or post a message on Twitter (@bioontologies) or our LinkedIn Group (https://www.linkedin.com/groups/13998260/).

Previous ISMB Meetings

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