SWAT4HCLS 2025
Semantic Web Applications and Tools for Health Care and Life Sciences 2025

Table of Contents

• Preface
  Summary: There were 59 papers submitted for peer-review to this workshop. Out of these, 23 papers were accepted s as long or short paper for this volume. The volume also contains the papers of the demonstration and poster tracks.

Long paper

• The Pistoia Alliance Pharma General Ontology: Experience using LinkML in Pharma 1–10
  Joshua Valdez, Philippe Rocca-Serra, Markus Hartmann, Darko Hric, Asiyah Yu Lin, Birgit Meldal, Peter McQuilton, Riccardo Mariani, Martin Romacker, Giovanni Nisato, Ben Gardner
• Biomedical Ontology Matching using Relational Graph Neural Networks and RDFs Meta-Path Rules 11–20
  Shervin Mehryar, Julie Loesch, Emma Pinckers, Alan van den Akker, Yannick Damoiseaux, Athanasios Stavrinopoulos, Nikola Prianikov, Remzi Celebi
• Semantic Beacons: a framework to support federated querying over genomic variants and public Knowledge Graphs 21–32
  Alexandrina Bodrug-Schepers, Hugo Chabane, Gabriela Montoya, Patricia Serrano-Alvarado, Richard Redon, Alban Gaignard
• HERO-Genomics: An Ontology for Integration and Access of Multicenter Genomic Data 33–42
  Mirco Cazzaro, Ivo G. Gut, Laura Menotti, Manuel Rueda, Gianmaria Silvello
• Enhancing GISMo: Integrating Recipe Contexts into a Graph-Based Ingredient Substitution Module 43–53
  Julie Loesch, David Schimmel, Funda Erdem, Deryanur Kalkavan, Zeki Bilgin, Remzi Celebi
• PubChemRDF on the Google Cloud Platform 54–66
  Sunghwan Kim, Bo Yu, Jia He, Qingliang Li, Tiejun Cheng, Siqian He, Hannah Bast, Johannes Kalmbach, Evan E Bolton
• Treating Query Graphs As Connecting Trees Mapping SPARQL Queries to FHIR API 67–74
  Eric Prud'hommeaux, Jerven Bolleman, Claude Nanjo
• FAIR Linked Data Framework for Glioblastoma Researc 75–84
  Zoi Katsirea, Samira Osterop, Valérie Dutoit, Tong Li, Etienne Doumazane, Stephane Pages, Omer Ali Bayraktar, Josh Moore, Andra Waagmeester, Tannia Gracia
• Quality issues on mappings between ICD10 and SNOMED CT 85–91
  Emiliano Reynares, Andrea Splendiani
• Imaging and curation of human TB lung tissue with linked data 92–99
  Gordon A. Wells, Kapongo Lumamba, Kievershen Nargan, Delon Naicker, Ashendree Govender, Rajhmun Madansein, Kameel Maharaj, Mpumelelo Msimang, Paul V Benson, Threnesan Naidoo, Zoi Katsirea, Tannia Gracia, Fani Memi, Josh Moore, Andra Waagmeester, Adrie J. Steyn
• Judgment Day: Symbolic AI versus Neuro-Symbolic AI in a Usability Study with UK Junior Doctors 100–114
  Mercedes Arguello Casteleiro, Chloe Henson, Manoj Kulshrestha, Diego Maseda Fernandez, Julio Des Diz, Carlos Sevillano Torrado, Nava Maroto, Maria Jesus Fernandez Prieto, Tim Furmston, Chris Wroe, John Keane, Robert Stevens

Short paper

• Trap of Time: Historical Common Names to Modern Taxonomy Mapping using LLMs 115–120
  Jan Fillies, Naouel Karam, Alois Wieshuber, Giada Matheisen, Malte Rehbein, Belen Escobari, Sarah Fischer, Adrian Paschke
• A multi-modal and temporal antibiotic resistance knowledge graph 121–125
  Brieuc Quemeneur, Audrey Bihouée, Samuel Chaffron, Claudine Médigue, Hervé Ménager, Alban Gaignard,
• Exploring Vendor-Neutral SMART on FHIR Infrastructure for Secure Data Exchange in Research and Patient Care 126–131
  Katja Hoffmann, Eveline Prochaska, Markus Wolfien, Martin Sedlmayr
• A Resolution-Alignment-Completeness System for Diagnosis Code Imputation in Clinical Knowledge Graphs 132–136
  Shervin Mehryar, Özge Erten, Tsvetan Asamov, Svetla Boytcheva, Remzi Çelebi,
• LLM-Based Ontology Mapping for Privacy-Preserving Healthcare Data Management 137–142
  Maria Papoutsoglou, Apostolos Mavridis, Stergios Tegos, Christos Anastasiou, Georgios Meditskos
• Utilization of Semantic Technologies to Achieve Interoperability Between Dental Data and EHRs: A Proof of Concept 143–147
  Hugo Lebredo, Ruben del Rey Álvarez, Jose Emilio Labra-Gayo,
• Leveraging Zarr to handle RDF data 148–152
  Ángel Iglesias Préstamo, Diego Martín Fernández, Jose Emilio Labra-Gayo, Josh Moore
• RDF resources for biomedical research 153–156
  Mayumi Kamada, Shuichi Kawashima, Toshiaki Katayama
• From Clinical Data to Discovery: integration of Beacon v2 with OMOP-CDM 157–159
  Sergi Aguiló-Castillo, Alberto Labarga, Miguel Ángel Mayer, Juan Manual Ramírez-Anguita, Oriol López-Doriga Sagales, Aurora Moreno-Racero, Liina Nagirnaja, Dmitry Repchevski, Salvador Capella-Gutierrez, Jordi Rambla
• Merging and Validating Health Ontologies: A Framework for Ontological Integration and Evaluation 160–165
  Safaa Menad, Saïd Abdeddaïm, Fatima Lina Soualmia,
• GlyCosmos: An Integrated Semantic Knowledge Base for Glycoscience 166–171
  Sunmyoung Lee, Yasunori Yamamoto, Achille Zappa Kiyoko F. Aoki-Kinoshita
• Comparison of Cardiovascular Disease Trajectories: A France vs Nordic countries’ perspective under the HealthData@EU EHDS project 172–176
  Gayo Diallo, Arti Rawat, Anna-Leena Vuorinen, Rachel B. Forster, Adrian G. Zucco, Tibor V. Varga, Andrea Ganna

Demonstration

• Leveraging AI Agents for Efficient Data Annotation 177–179
  Chang In Moon, Anh Nguyet Vu, Alex Verbitsky, Brian Dennis, Chris Harman, Mark Weston, Mohammed Eslami, Patrick Boutet, Christina Parry, Jineta Banerjee, John Hill, Jay Hodgson, Alberto Pepe, Milen Nikolov, Sonia Carlson, Robert J. Allaway
• QASAR: A quality assurance tool for semantic resources 180–182
  Gonzalo Nicolás Martínez, Francisco Abad-Navarro, Manuel Quesada-Martínez, Astrid Duque Ramos, Belén Juanes Cortés, Jesualdo Tomás Fernández Breis
• MetaTron: Streamlining Collaborative Annotation for Biomedical Documents 183–185
  Ornella Irrera, Stefano Marchesin, Gianmaria Silvello
• Demonstration: The MeDaX-KG on FHIR 186–187
  Ilya Mazein, Tom Gebhardt, Sebastian Berthe, Kai Fitzer, Ron Henkel, Markus Mandalka, Seyed Reza Mazlooman, Lea Michaelis, Dagmar Waltemath, Benjamin Winter, Judith A.H. Wodke
• The Wheat and Rice Genomics Scientific Literature Knowledge Graphs 188–190
  Nadia Yacoubi Ayadi, Franck Michel, Robert Bossy, Marine Courtin, Bill Gates Happi Happi, Pierre Larmande, Claire Nedellec, Catherine Faron
• Collaborative management of Semantic Web datasets: maintaining EuroSciVoc with VocBench and ShowVoc 191–193
  Anikó Gerencsér, Baya Remaoun, Enrico Bignotti
• Using NFDI4Health Local Data Hub and Metadata-Schema for clinical research information management 194–196
  Frank Meineke, Matthias Löbe, René Hänsel, Masoud Abedi, Xiaoming Hu, Martin Golebiewski
• Demonstrating Study Discovery and Exploration Through a Knowledge Graph 197–198
  Lea Gütebier, Dagmar Waltemath, Ron Henkel

Poster paper

• Semantifying Genomic Variant Data: VCF to RDF Conversion Framework 199–200
  Elias Crum, Ruben Taelman, Bart Buelens, Gokhan Ertaylan, Ruben Verborgh
• Integrating Data Treasures – The First Knowledge Graphs of the DSMZ Digital Diversity Databases 201–203
  Julia Koblitz, Lorenz Christian Reimer,
• Predicting Clinical Remission in Crohn’s Disease: A Comparative Study of Expert-Generated and Computer-Generated Bayesian Networks 204–206
  Yomi Okegunna, Maija Utriaine, Manon .J.J. Cloots, Jiaxu Zhang, Inigo Bermejo, Loriane .M.M. Verleye, Marjolijn Duijvestein, Zlatan Mujagic, Andre Dekker, Marieke .J. Pierik, Rianne R.R Fijten
• Assessment of metadata descriptors of AI-ready datasets 207–209
  Jerven Bolleman, Leyla Jael Castro, Alban Gaignard, Agoritsa Kalampaliki, Edwin Jun Kiat Ong, Núria Queralt-Rosinach, Nelson David Quiñones Virgen, Rohitha Ravinder, Dhwani Solanki, David Steinberg, Claus Weiland, Daphne Wijnbergen
• Development of in-context methods with Large Language Models for statement validation: towards semi-automated ontology learning in novel biological contexts 210–212
  James Wilsenach, Sebastian Ahnert
• Anonymization Ontology: A Privacy-Preserving Framework for GDPR-Compliant Anonymization of Personal Health Data 213–215
  Noopur Rai, Marta Dembska, Sirko Schindler
• FAIR principles: from seed supermarkets to germplasm data centers 216–216
  Alberto Cámara Ballesteros, Santiago Moreno Vazquez, Mark D. Wilkinson
• FAIR Software as a Service: Deployment of FAIR infra made easy 217–219
  Rick Overkleeft, Sander van Boom, Eric Prud'Hommeaux, Kees Burger, Jip Fransen, Marc Padros Goossens, Luiz Bonino da Silva Santos, Rajaram Kaliyaperumal, Marco Roos
• AgroLD: a Knowledge Graph for the Plant Sciences 220–221
  Pierre Larmande, Bertrand Pitollat, Ndomassi Tando, Yann Pomie, Bill Gates Happi Happi, Valentin Guignon
• DATOS.CAT: Improving the level of the interoperability of GCAT in line with the FAIR principles with OntoBridge, dsOMOP and OMOP Beacon 222–223
  Aikaterini Lymperidou, David Sarrat-González, Ramon Mateo-Navarro, Guillem Bracons-Cucó, Aurora Moreno-Racero, Jordi Rambla de Argila, Liina Lagirnaja, Carles Hernandez-Ferrer, Salvador Capella-Gutierrez, Santiago Frid, Juan R González, Rafael de Cid
• An Automated Framework to generate pairs of Natural Language Questions and SPARQL Queries from Common RDF Graph Patterns 224–226
  Julio C. Rangel, Tarcisio Mendes de Farias, Yamamoto Yasunori, Ana Claudia Sima, Norio Kobayashi
• A Knowledge Graph for Enhanced Study Discovery and Semantic Exploration 227–229
  Lea Gütebier, Dagmar Waltemath, Ron Henkel
• OMExcavator: a tool for exporting and connecting domain-specific metadata in a wider knowledge graph 230–232
  Stefan Dvoretskii, Michele Bortolomeazzi, Christian Schmidt, Josh Moore, Klaus Maier-Hein, Marco Nolden
• Towards dynamic consent and transparent access tracking for decentralized health records using the SOLID framework 233–234
  Kalliopi Kastampolidou, Achilleas Chytas, Pantelis Natsiavas
• Lowering Barriers to FAIR Data: A User-Friendly Tool for Semantic Data Transformation 235–237
  Karolis Cremers, César Bernabé, Daphne Wijnbergen, Rosa Zwart, Anna Niehues, Marco Roos
• RDF Portal: Enhancing Accessibility and Interoperability of Life Science RDF 238–239
  Shuichi Kawashima, Yasunori Yamamoto, Hirokazu Chiba, Yuki Moriya, Toshiaki Katayama
• FAIR in practice: minimum metadata schema for bioinformatics analytics by machines 240–241
  Daphne Wijnbergen, Núria Queralt-Rosinach, Valérie Barbié, Emma Verkinderen, Nirupama Benis, Annika Jacobsen, Peter A.C. 't Hoen, Claudio Carta, Marco Roos, Eleni Mina
• Constructing a synonymous URI dictionary in life sciences 242–244
  Yasunori Yamamoto, Takatomo Fujisawa
• Extended RDF support for Biomedical Knowledge Graphs in pyBioDataFuse: on-the-fly RDF graph generation and new resource annotators 245–248
  Javier Millán Acosta, Egon Willighagen, Yojana Gadiya, Tooba Abbassi-Daloii