# SWAT4HCLS 2024 Semantic Web Applications and Tools for Health Care and Life Sciences 2024

Event
  15th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences
Location
  Leiden, The Netherlands
Date
  February 20th to 26th, 2024

Edited by
  Marco Roos1
  Annika Jacobsen2
  Andrea Splendiani3
  M. Scott Marshall4
  Andra Waagmeester5
  Leyla Jael García Castro6
  Katherine Wolstencroft7
  Kristina Hettne8
  Rutger Vos9

- 1Leiden University Medical Centre, The Netherlands
- 2Leiden University Medical Centre, The Netherlands
- 3IQVIA, CH
- 4TRKKN, The Netherlands
- 5Micelio, Belgium
- 6ZB MED, Germany
- 7Leiden University, The Netherlands
- 8Leiden University, The Netherlands
- 9Naturalis, The Netherlands

## Table of Contents

1. Preface

   Summary: There were 25 papers, of which 20 regular papers and 5 short papers, submitted for peer-review to this workshop. Out of these, 15 papers, of which 9 regular and 6 short papers, were accepted for this volume.

### Session 0: Regular Papers

1. Exploring the role of generative AI in constructing knowledge graphs for drug indications with medical context
   Pages
     1–10
   Authors
     Reham Alharbi
     Umair Ahmed
     Daniil Dobriy
     Weronika Łajewska
     Laura Menotti
     Mohammad Javad Saeedizade
     Michel Dumontier
2. SPHN strategy to unravel the semantic drift between versions of standard terminologies
   Pages
     11–22
   Authors
     Deepak Unni
     Vasundra Touré
     Philip Krauss
     Katrin Crameri
     Sabine Österle
3. Representation and comparison of chemotherapy protocols with ChemoKG and graph embeddings
   Pages
     23–35
   Authors
     Jong Ho Jhee
     Alice Rogier
     Dune Giraud
     Emma Pinet
     Brigitte Sabatier
     Bastien Rance
     Adrien Coulet
4. SPARQL generation: an analysis on fine-tuning OpenLLaMA for Question Answering over a Life Science Knowledge Graph
   Pages
     36–45
   Authors
     Julio C. Rangel
     Tarcisio Mendes de Farias
     Ana Claudia Sima
     Norio Kobayashi
5. Explaining Graph Neural Network predictions for drug repurposing
   Pages
     46–55
   Authors
     Julie Loesch
     Yang Yang
     Pelinsu Ekmekci
     Michel Dumontier
     Remzi Celebi
6. Refining SemOpenAlex concept ontology: A constraint-aware approach via knowledge graph embeddings and SKOS constraints
   Pages
     56–65
   Authors
     Özge Erten
     Shervin Mehryar
     Bo Xiong
     Remzi Çelebi
     Christopher Brewster
7. Extracting shapes from large RDF data collections
   Pages
     66–75
   Authors
     Daniel Fernández-Álvarez
     Yasunori Yamamoto
     Jose Emilio Labra-Gayo
     Andra Waagmeester
8. Unlocking semantics as a FAIR implementation profile. Reflections and lessons learned building user-centric semantic authoring applications
   Pages
     76–87
   Authors
     Selena Baset
     Didier Clement
9. Automated drug repurposing workflow for rare diseases
   Pages
     88–106
   Authors
     Carmen A. T. Reep
     Katherine Wolstencroft
     Eleni Mina
     Núria Queralt-Rosinach

### Session 1: Short Papers

1. Bridging clinical and genomic knowledge: An extension of the SPHN RDF Schema for seamless integration and FAIRification of omics data
   Pages
     107–115
   Authors
     Eelke van der Horst
     Deepak Unni
     Femke C. Kopmels
     Jan Armida
     Vasundra Touré
     Wouter Franke
     Katrin Crameri
     Elisa Cirillo
     Sabine Österle
2. Take CARE of your patient data. Clinical And Registry Entries (CARE) Semantic Model
   Pages
     116–123
   Authors
     Pablo Alarcón-Moreno
     Mark Denis Wilkinson
3. Applying the RDA Data Maturity Model on the Core Dataset of the German Medical Informatics Initiative
   Pages
     124–128
   Authors
     Lea Michaelis
     Esther Thea Inau
     Michael Rusongoza Muzoora
     Judith A. H. Wodke
     Thomas Ganslandt
     Sylvia Thun
     Dagmar Waltemath
4. A metadata profile to promote Real-World Data discoverability
   Pages
     129–133
   Authors
     Emiliano Reynares
     Andrea Splendiani
     Hanne van Ballegooijen
5. Analyzing SPARQL query logs: A study on schema coverage and query content
   Pages
     134–139
   Authors
     Maryam Mohammadi
     Michel Dumontier
6. Ontology enhanced FAIR Data Point searches
   Pages
     140–144
   Authors
     Xiaofeng Liao
     Coos Baakman
     Kees Burger
     Luiz Olavo Bonino da Silva Santos
     Peter A. C. 't Hoen

### Session 2: Poster Papers

1. Temporal data modeling evaluation in knowledge graphs: A healthcare use case
   Pages
     145–146
   Authors
     Sepideh Hooshafza
     Gaye Stephens
     Mark A. Little
     Beyza Yaman
2. Recognition of biodiversity-related named entities by fine-tuning general-domain BERT-based language models
   Pages
     147–148
   Authors
     Geilah T. Tabanao
     Andrew Miguel V. Pagdanganan
     Riza Batista-Navarro
     Roselyn S. Gabud
3. Application of the RDF framework to integrate heterogenous experimental data of a large chemo- and biodiverse collection from a collaborative research project
   Pages
     149–152
   Authors
     Frederic Burdet
     Luis-Manuel Quiros-Guerrero
     Olivier Kirchhoffer
     Jahn Nitschke
     Pierre-Marie Allard
     Louis-Felix Nothias
     Arnaud Gaudry
     Sébastien Moretti
     Robin Engler
     Emerson Ferreira Queiroz
     Nabil Hanna
     Chunyan Wu
     Antonio Grondin
     Bruno David
     Thierry Soldati
     Christian Wolfrum
     Erick Carreira
     Jean-Luc Wolfender
     Marco Pagni
     Florence Mehl
4. INDEX: the Intelligent Data Steward Toolbox. Utilizing Large Language Model embeddings for automated data harmonization
   Pages
     153–154
   Authors
     Tim Adams
     Mohamed Aborageh
     Yasamin Salimi
     Holger Fröhlich
     Marc Jacobs
5. LARA - embracing almost fully automated experimentation from ground up by using semantic web technologies in Life Sciences
   Pages
     155–156
   Authors
     Mark Doerr
     Stefan Born
6. Personalised medical content delivery to support patient empowerment based on knowledge graphs
   Pages
     157–158
   Authors
     Christine Kakalou
     Christina Karamanidou
     Theodore Dalamagas
     Manolis Koubarakis
7. Achieving data FAIRification in a distributed analytics research platform for rare diseases
   Pages
     159–160
   Authors
     Anna Bernasconi
     Cinzia Cappiello
     Stefano Ceri
     Pietro Pinoli
8. BioDataFuse: Enhancing data interoperability through modular queries and knowledge graph construction
   Pages
     161–164
   Authors
     Tooba Abbassi-Daloii
     Yojana Gadiya
     Ammar Ammar
     Egon Willighagen
     Ana Claudia Sima
     Hasan Balci
9. Construction of a knowledge graph for food health claims
   Pages
     165–166
   Authors
     Remzi Celebi
     Ilse van Lier
     Alie de Boer
     Michel Dumontier
10. Personalized medicine through personal data pods
    Pages
      167–168
    Authors
      Elias Crum
      Ruben Taelman
      Bart Buelens
      Gokhan Ertaylan
      Ruben Verborgh
11. Designing a FAIRification game for Research Software
    Pages
      169–170
    Authors
      Rohitha Ravinder
      Dhwani Solanki
      Claudio Carta
      Bruna dos Santos Vieira
      Johannes Keller
      Marco Roos
      Leyla Jael Castro
12. Causal discovery on Health-related Quality of Life of cancer patients
    Pages
      171–172
    Authors
      Maria Ganopoulou
      Efstratios Kontopoulos
      Konstantinos Fokianos
      Lefteris Angelis
      Ioannis Kotsianidis
      Theodoros Moysiadis
13. CHIST-ERA Triple: improving data interoperability and federation across RDF knowledge graphs and Solid Pods
    Pages
      173–175
    Authors
      Jerven Bolleman
      Elias Crum
      Iulian Dragan
      Jakub Galgonek
      Mark Ibberson
      Tarcisio Mendes de Farias
      Marek Moos
      Marco Pagni
      Ruben Taelman
      Jiří Vondrášek
      Ana Claudia Sima
14. Updating the SynthDNASim tool to create diverse synthetic DNA datasets
    Pages
      176–177
    Authors
      Caitlin Jenster
      Rick Overkleeft
      Núria Queralt Rosinach
15. FAIR for automatic federated omics analysis
    Pages
      178–179
    Authors
      Daphne Wijnbergen
      Georgios Malamas
      Marco Roos
      Eleni Mina
16. DATOS-CAT: Methodologies for the standardization, integration and analysis of population-based biomedical data using semantic technologies
    Pages
      180–182
    Authors
      Judith Martinez-Gonzalez
      Guillem Bracons Cucó
      Aikaterini Lymperidou
      Xavier Escribà-Montagut
      Marta Huertas
      Ramon Mateo-Navarro
      David Sarrat-González
      Santiago Frid
      Rafael de Cid
      Juan Ramón González
      Alberto Labarga
17. OMOP-CDM mapping to RDF/OWL: Attempting to bridge the OHDSI ecosystem and the Semantic Web world
    Pages
      183–184
    Authors
      Achilleas Chytas
      Nick Bassiliades
      Pantelis Natsiavas
18. OpenPVSignal Knowledge Graph: An openly available data source for pharmacovigilance signal reports
    Pages
      185–186
    Authors
      Achilleas Chytas
      Pantelis Natsiavas
19. FAIR Service Descriptions: enriching life science SPARQL endpoints
    Pages
      187–188
    Authors
      Jerven Bolleman
      Alan Bridge
      Nicole Redaschi
20. Integration of variation data through SPARQL Micro-Services
    Pages
      189–190
    Authors
      Frederic Metereau
      Franck Michel
      Pierre Larmande
      Guilhem Sempere
      Catherine Faron
21. Nanosafety data made interoperable using semantic modeling and linked-data knowledge graphs
    Pages
      191–191
    Authors
      Ammar Ammar
      Egon Willighagen
22. Representing bioinformatics Nextflow workflows in RO-Crate: challenges and opportunities
    Pages
      192–193
    Authors
      George Marchment
      Marie Schmit
      Clémence Sebe
      Frédéric Lemoine
      Hervé Ménager
      Sarah Cohen-Boulakia
23. The approach of IQVIA to ontologies for healthcare and life sciences
    Pages
      194–195
    Authors
      Andrea Splendiani
      Emiliano Reynares
      Anthony Reckard
24. MLentory, an FDO registry for machine learning models
    Pages
      196–197
    Authors
      Dhwani Solanki
      Nelson Quiñones
      Dietrich Rebholz-Schuhmann
      Leyla Jael Castro
25. There and back again: RDF as a bridge to domain-platforms like OMERO
    Pages
      198–199
    Authors
      Josh Moore
      Andra Waagmeester
      Kristina Hettne
      Katherine Wolstencroft
      Susanne Kunis
26. MeDaX Prototype v0.2
    Pages
      200–201
    Authors
      Ilya Mazein
      Sarah Braun
      Tom Gebhardt
      Ron Henkel
      Lea Michaelis
      Dagmar Waltemath
      Judith A. H. Wodke
27. A semantic design for the biological processes associated with intrinsically disordered proteins
    Pages
      202–203
    Authors
      Atsuko Yamaguchi
      Yumiko Kado
      Shigetaka Sakamoto
      Satoshi Fukuchi
      Motonori Ota
28. Make RDF data more inter-connectable
    Pages
      204–205
    Authors
      Yasunori Yamamoto
      Takatomo Fujisawa
29. FAIR Data Cube, a FAIR data infrastructure for integrated multi-omics data analysis
    Pages
      206–207
    Authors
      Xiaofeng Liao
      Yuliia Orlova
      Cenna Doornbos
      Anna Niehues
      Casper de Visser
      Junda Huang
      Thomas H. A. Ederveen
      Purva Kulkarni
      K. Joeri van der Velde
      Morris A. Swertz
      Martin Brandt
      Alain J. van Gool
      Peter A. C. 't Hoen
30. FAIR Software as a Service: Combining tools to implement FAIR for clinical data platforms
    Pages
      208–209
    Authors
      Rick Overkleeft
      Sander van Boom
      Eric Prud'Hommeaux
      Kees Burger
      Jip Fransen
      Teus Kappen
      Luiz Bonino da Silva Santos
      Rajaram Kaliyaperumal
      Marco Roos
31. Vision for modular taxonomy production at Elsevier: The VOICE project
    Pages
      210–211
    Authors
      Wytze J. Vlietstra
      Matthias Albus
      Nick Drummond
      Simon Jupp
      George Georghiou

We offer a BibTeX file for citing papers of this workshop from LaTeX.