|  | Vol-3603 urn:nbn:de:0074-3603-6 Copyright © 2023 for the individual papers by the papers' authors. Copyright © 2023 for the volume as a collection by its editors. This volume and its papers are published under the Creative Commons License Attribution 4.0 International (CC BY 4.0).

# ICBO 2023
International Conference on Biomedical Ontologies 2023

### Proceedings of the International Conference on Biomedical Ontologies 2023
together with the Workshop on Ontologies for Infectious and Immune-Mediated Disease Data Science (OIIDDS 2023)
and the FAIR Ontology Harmonization and TRUST Data Interoperability Workshop (FOHTI 2023)

### Brasília, Brazil, August 28 - September 1,2023.

Edited by

### Fernanda Farinelli *
Amanda Damasceno de Souza **
Eduardo Ribeiro Felipe ***

* University of Brasilia (UnB),Faculty of Information Science, Brasilia, Brazil
** FUMEC University, Postgraduate Program in Information and Communication Technology and Knowledge Management (PPGTICGC), Belo Horizonte, Brazil
*** Federal University of Itajubá (UNIFEI), Institute of Technological Sciences, Itabira, Brazil

## 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

2023-12-13: submitted by Fernanda Farinelli, metadata incl. bibliographic data published under Creative Commons CC0
2023-12-31: published on CEUR Workshop Proceedings (CEUR-WS.org, ISSN 1613-0073) |valid HTML5|