Programme: ISMB/ECCB 2025, Liverpool, UK

Tuesday, July 22 (joint session with BOSC)

11:20  BOSC-BOKR joint session introduction

11:21  Keynote: Open Knowledge Bases in the Age of Generative AI. Chris Mungall (Lawrence Berkeley National Laboratory)

12:20  textToKnowledgeGraph: Generation of Molecular Interaction Knowledge Graphs Using Large Language Models for Exploration in Cytoscape. Favour James (Obafemi Awolowo University)

12:40  BMFM-RNA: An Open Framework for Building and Evaluating Transcriptomic Foundation Models built on Biomed-Multi-Omic. Bharath Dandala (IBM)

14:00  BioPortal: a rejuvenated resource for biomedical ontologies. J. Harry Caufield (Lawrence Berkeley National Laboratory)

14:20  Formal Validation of Variant Classification Rules Using Domain-Specific Language and Meta-Predicates. Michael Bouzinier (Forome Association, Harvard University)

14:40  BioChatter: An open-source framework integrating knowledge graphs and large language models for Accessible Biomedical AI. Sebastian Lobentanzer (Helmholtz Munich)

15:00  Applications of Bioschemas in FAIR, AI and knowledge representation. Nick Juty (The University of Manchester)

15:20  RO-Crate: Capturing FAIR research outputs in bioinformatics and beyond. Phil Reed (The University of Manchester)

15:40  10 years of the AberOWL ontology repository: moving towards federated reasoning and natural language access. Robert Hoehndorf (KAUST)

16:40  The global biodata infrastructure: how, where, who, and what? Guy Cochrane (Global Biodata Coalition)

16:50  Panel: Data Sustainability. Chaired by Chris Mungall

17:50  Closing remarks

Wednesday, July 23

11:20  Knowledge-Graph-driven and LLM-enhanced Microbial Growth Predictions. Marcin Joachimiak (Lawrence Berkeley National Laboratory)

11:40  ProDiGenIDB: a unified resource of disease-associated genes, their protein products, and intrinsic disorder annotations. Jovana Kovacevic (University of Belgrade)

12:00  Causal knowledge graph analysis identifies adverse drug effects. Sumyyah Toonsi (KAUST)

12:20  CROssBARv2: A Unified Biomedical Knowledge Graph for Heterogeneous Data Representation and LLM-Driven Exploration. Erva Ulusoy (Hacettepe University)

12:40  Benchmarking Data Leakage on Link Prediction in Biomedical Knowledge Graph Embeddings. Galadriel Brire (Aix-Marseille University)

12:45  A machine learning framework for extracting and structuring biological pathway knowledge from scientific literature. Mun Su Kwon (KAIST)

12:50  Poster Madness

14:00  Proceedings paper: ScGOclust: leveraging gene ontology to find functionally analogous cell types between distant species. Yuyao Song (EMBL-EBI)

14:20  Integrating autoantibody-related knowledge in an ontology populated using a curated dataset from literature. Fabien Maury (Inserm)

14:40  Ontology pre-training improves machine learning predictions of aqueous solubility and other metabolite properties. Charlotte Tumescheit (University of Zurich, SIB)

15:00  Building the Aging Biomarkers Ontology and Its Applications in Aging Research. Hande McGinty (Kansas State University)

15:20  Discovering cellular contributions to disease pathogenesis in the NLM Cell Knowledge Network. Richard Scheuermann (National Library of Medicine)

15:40  Cat-VRS for Genomic Knowledge Curation: A Hyperintensional Representation Framework for FAIR Categorical Variation. Daniel Puthawala (Nationwide Children's Hospital)

16:40  Keynote: Knowledge Graphs: Theory, Applications and Challenges. Ian Horrocks (University of Oxford)

17:40  Bridging Language Barriers in Bio-Curation: An LLM-Enhanced Workflow for Ontology Translation into Japanese. Mark Streer (SciBite)

17:45  Enabling FAIR Single-Cell RNAseq Data Management with COPO. Felix Shaw (Earlham Institute)

17:50  Cancer Complexity Knowledge Portal: A centralized web portal for finding cancer related data, software tools, and other resources. Susheel Varma (Sage Bionetworks)

17:55  COSI closing remarks

Posters

Using the Linked Data Modeling Language and the Oral Health and Disease Ontology to Represent Dental Care-Related Fear and Anxiety Studies. Finn Wilson (University at Buffalo)

sCentInDB: A database of essential oil chemical profiles of Indian medicinal plants. Shanmuga Priya Baskaran (Institute of Mathematical Sciences, Chennai)

Modeling Human Functional Networks with Gene Ontology Causal Activity Models (GO-CAMs). Cristina Casals-Casas (Swiss Institute of Bioinformatics)

TransFusionKG: Integrating TransE and Graph Denoising Transformers for Structured Drug Repositioning. Betl Erkantarcı (Abdullah Gl University)

In-silico protocols for reproducibility of machine learning approaches. Dhwani Solanki (ZB MED Information Centre for Life Sciences)

FAIRisation of Bioconductor packages using the EDAM ontology. Claire Rioualen (Institut Franais de Bioinformatique)

KGATE, an Autoencoder Training Environment for exploring and benchmarking Knowledge Graph Embedding models. Benjamin Loire (Servier)

Knowledge Graph Frameworks for Biomedical Discovery: Case Studies in Population Health and Precision Therapeutics. Chuming Chen (University of Delaware)

Source: ISCB ISMB/ECCB 2025 programme (BOKR track and poster listings).

Submission Types

Bio-Ontologies and Knowledge Representation (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 and Knowledge Representation will be in its 28th year at ISMB 2025 (https://www.iscb.org/ismbeccb2025), which will be held in-person and online between July 20-24, 2025 and will feature two days of exciting keynotes and cutting-edge research.

Submissions

We invite the submissions of proceedings papers (9 pages), abstracts (1 page) which will be reviewed and selected abstracts invited for oral or poster presentation.

The COSI covers these topics:

• New knowledge bases, knowledge graphs, and ontologies

• Methods that use knowledge bases, knowledge graphs, and ontologies

• Applications using knowledge bases, knowledge graphs, and ontologies

• Methods to improve knowledge bases, knowledge graphs, and ontologies

in bioinformatics, biomedical/life science research, health informatics, and healthcare

Examples include (but are not limited to):

• Novel knowledge bases, knowledge graphs, and ontologies in bioinformatics

• Ontologies and knowledge graphs in annotations, mapping applications, and metadata standards

• FAIR data systems and application of ontologies and other linked open data

• Bio-curation platforms

• Evaluation of knowledge graphs, ontologies, and knowledge bases

• Ontologies, knowledge representation, and reasoning

• Machine learning/artificial intelligence and knowledge representation

• Neuro-symbolic methods in bioinformatics

• Semantic Web-enabled applications

• Ontologies for biomedical/life science research, health informatics, and healthcare

Submissions can be made on the ISMB site (https://www.iscb.org/ismbeccb2025). For proceedings, please follow the instructions provided on the ISMB site. For all other submissions, please prepare your submission using the Bio-Ontologies and Knowledge Representation templates (https://www.bio-ontologies.org.uk/2025-meeting).

All submissions are reviewed (review criteria provided on the Bio-Ontologies and Knowledge Representation website). Based on the review process, abstracts will be selected for oral or poster presentation at the Bio-Ontologies and Knowledge Representation COSI.

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.

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/).

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