CEUR-WS
Identifier
https://ceur-ws.org/Vol-3890/
Volume
Vol-3890
URN
urn:nbn:de:0074-3890-8
Language
eng
License
CC BY Copyright © 2024 for the individual papers by the papers' authors. Copyright © 2024 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 ) .

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
to
Edited by
Marco Roos 1
Annika Jacobsen 2
Andrea Splendiani 3
M. Scott Marshall 4
Andra Waagmeester 5
Leyla Jael García Castro 6
Katherine Wolstencroft 7
Kristina Hettne 8
Rutger Vos 9
  • 1 Leiden University Medical Centre , The Netherlands
  • 2 Leiden University Medical Centre , The Netherlands
  • 3 IQVIA , CH
  • 4 TRKKN , The Netherlands
  • 5 Micelio , Belgium
  • 6 ZB MED , Germany
  • 7 Leiden University , The Netherlands
  • 8 Leiden University , The Netherlands
  • 9 Naturalis , 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.