ICBO 2023
International Conference on Biomedical Ontologies 2023

Table of Contents

• Preface
  Summary: There were 24 papers submitted for peer-review to the main conference. Out of these, 20 papers were accepted for this volume: 14 as regular/full papers, 2 as short papers, 4 as poster abstracts.
  
  Click here to download the full conference proceedings PDF.

Session 1: Main Conference

Full Papers

• Ontology-based Representation and Analysis of Conditional Vaccine Immune Responses Using Omics Data 1-12
  Anthony Huffman, Edison Ong, Tim Brunson, Nasim Sanati, Jie Zheng, Anna Maria Masci, Guanming Wu, Yongqun He
• Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition 13-24
  Sumyyah Toonsi, Senay Kafkas, Robert Hoehndorf
• An Extendible Realism-Based Ontology for Kinship 25-35
  Michael Rabenberg, Anuwat Pengput, Werner Ceusters
• Towards Principles of Ontology-Based Annotation of Clinical Narratives 36-47
  Stefan Schulz, Warren Del-Pinto, Lifeng Han, Markus Kreuzthaler, Sareh Aghaei Dinani, Goran Nenadic
• An Ontology for Mammography Screening Recommendation 48-59
  Cindy Acuña, Yasmine Anchén, Edelweis Rohrer, Regina Motz
• An Application of Natural Language Processing and Ontologies to Electronic Healthcare Records in the Field of Gynecology 60-69
  Amanda Damasceno de Souza, Fernanda Farinelli, Eduardo Ribeiro Felipe, Armando Sérgio de Aguiar Filho, Maurício Barcellos Almeida
• The Potential of Ontologies for the Empirical Assessment of Machine Learning Techniques in Operational Oceanography 70-81
  Enrique Wulff
• Concrete Names for Complex Expressions in Ontologies: A Survey of Biomedical Ontologies 82-93
  Christian Kindermann, Martin Georg Skjæveland
• Leveraging Biomedical Ontologies to Boost Performance of BERT-Based Models for Answering Medical MCQs 94-105
  Sahil, P Sreenivasa Kumar
• The OntoWoH Ontology - a Women's Health Reference Ontology Detailing the Fragment of Climacteric and Menopause 106-117
  Cilenir Carla de Carvalho, Andreia Soprani dos Santos, Silvia Das Dores Rissino, Susana Bubach, Maria Das Graças Da Silva Teixeira
• Using Ontology Embeddings With Deep Learning Architectures to Improve Prediction of Ontology Concepts From Literature 118-129
  Pratik Devkota, Somya Mohanty, Prashanti Manda
• KOSonto: an Ontology for Knowledge Organization Systems, Their Constituents, and Their Referents 130-141
  Jean Noël Nikiema, Fleur Mougin, Vianney Jouhet, Stefan Schulz
• Reuse and Enrichment for Building an Ontology for Obsessive-Compulsive Disorder 142-153
  Areej Muhajab, Alia Abdelmoty, Athanasios Hassoulas
• Version Control for Interdependent Ontologies: Challenges and First Propositions 154-165
  Paul Fabry, Adrien Barton, Jean-Francois Ethier

Short Papers

• Ontology-based Integration of Consumer Data and EHR Systems to Fill Gaps in Social Determinants of Health Data 166-172
  S. Clint Dowland, Melody Greer, Sudeepa Bhattacharyya, Mathias Brochhausen
• Beyond the Goods-Service Continuum 173-178
  Peter Koch, Barry Smith

Poster Abstracts

• A Method to Facilitate the Identification of FAIRification Objectives 179
  César Bernabé, Annika Jacobsen, Luiz O. Bonino da S.S., Marco Roos
• Taxonomy Proposal for Controlled Vocabulary Planning in the Pinakes Catalogue With Tematres 180
  Josina da Silva Vieira, Letícia Santos de Jesus, Tainá Batista de Assis
• The Interplay of Wikidata and the Cell Ontology 181
  Tiago Lubiana
• Tracking the Functional Effects of SARS-CoV-2 Genomic Variants: an Ontology-Driven Approach 182-183
  Madeline Iseminger, Muhammad Zohaib Anwar, Rhiannon Cameron, Damion Dooley, Paul Gordon, Emma Griffiths, Anoosha Sehar, Khushi Vora, William Hsiao

Session 2: Workshops, Tutorials and Software Demo

Workshop on Ontologies for Infectious and Immune-Mediated Disease Data Science (OIIDDS 2023)

• Ontology Development Strategies and the Infectious Disease Ontology Ecosystem 184-192
  Giacomo De Colle, Ali Hasanzadeh, John C. Beverley
• Integrating Declarative and Procedural Knowledge in Infectious Disease Scenario for Epidemiological Monitoring 193-198
  Evellin Cardoso
• Multi-Ontology framework of Maternal Milk for Immune Systems (MOMMIS) 199-203
  Emily Steliotes, Daniela Barile, Matthew Lange

Workshop on FAIR Ontology Harmonization and trust Data Interoperability (FOHTI 2023)

• An Interactive Dashboard for Ontology Quality Monitoring 204-210
  Avetis Mkrtchian, Petr Křemen

Tutorials Abstracts

• Natural Language Processing Tutorial for Biomedical Text Mining 211
  Senay Kafkas, Sumyyah Toonsi, Sakhaa Alsaedi
• BFO as a Top-Level Ontology for Information Systems Modeling 212
  Maurício B. Almeida, Jeanne L. Emygdio
• Ontology-Driven Conceptual Modeling with UFO, gUFO, and OntoUML 213
  Giancarlo Guizzardi

Software Demo Abstract

• Ontology Development in FHIR Resources with the Fast Evidence Interoperability Resources (FEvIR) Platform 214
  Brian S. Alper, Khalid Shahin, Joanne Dehnbostel, Cauê F. Monaco