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 Research 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