# SWAT4HCLS 2023 Semantic Web Applications and Tools for Health Care and Life Sciences 2023

Event
  14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023)
Location
  Basel, Switzerland
Date
  February 13th to 16th, 2023

Edited by
  Atsuko Yamaguchi1
  Andrea Splendiani2
  M. Scott Marshall3
  Chris Baker4
  Jerven Bolleman5
  Albert Burger6
  Leyla Jael Castro7
  Ole Eigenbrod8
  Sabine Österle5
  Martin Romacker9
  Andra Waagmeester10

- 1Tokyo City University, Japan
- 2IQVIA, Switzerland
- 3TRKKN Netherlands, Netherlands
- 4Rothamsted Research, UK
- 5Swiss Institute of Bioinformatics, Switzerland
- 6Heriots-Watt University, UK
- 7ZB MED Information Centre for Life Sciences, Germany
- 8Roche, Germany
- 9Roche, Switzerland
- 10Micelio, Belgium

## Table of Contents

- Preface

  Summary: There were 22 papers submitted for peer-review to this workshop. Out of these, 14 papers were accepted for this volume.

- Using BPMN for medical guidelines that integrate with FHIR-RDF
  Pages
    1–10
  Authors
    Gerhard Kober
    Livio Robaldo
    Adrian Paschke
- Privacy-Preserving Dashboard for F.A.I.R Head and Neck Cancer data supporting multi-centered collaborations
  Pages
    11–21
  Authors
    Varsha Gouthamchand
    Ananya Choudhury
    Frank Hoebers
    Frederik Wesseling
    Mattea Welch
    Sejin Kim
    Benjamin Haibe-Kains
    Joanna Kazmierska
    Andre Dekker
    Johan Van Soest
    Leonard Wee
- Generating Knowledge Graph Based Explanations for Drug Repurposing Predictions
  Pages
    22–31
  Authors
    Elif Ozkan
    Remzi Celebi
    Arif Yilmaz
    Vincent Emonet
    Michel Dumontier
- Resource Description Framework (RDF) Modeling of Named Entity Co-occurrences Derived from Biomedical Literature in the PubChemRDF
  Pages
    32–41
  Authors
    Qingliang Li
    Sunghwan Kim
    Leonid Zaslavsky
    Tiejun Cheng
    Bo Yu
    Evan E. Bolton
- FSO: Food Safety Monitoring Ontology
  Pages
    42–51
  Authors
    Arif Yilmaz
    Raghavendra Naidu
    Christopher Brewster
- Attention for Multi-Ontology Concept Recognition
  Pages
    52–61
  Authors
    Lorcán Pigott-Dix
    Robert P. Davey
- BiodivBERT: a Pre-Trained Language Model for the Biodiversity Domain
  Pages
    62–71
  Authors
    Nora Abdelmageed
    Felicitas Löffler
    Birgitta König-Ries
- FAIR Functional Enrichment: Assessing and Modelling Provenance in Omics Results
  Pages
    72–81
  Authors
    Yi Chen
    Fons J. Verbeek
    Katherine J. Wolstencroft

### Short Papers

- Predicting missing annotations in Gene Ontology with Knowledge Graph Embeddings and True Path Rule
  Pages
    82–86
  Authors
    Özge Erten
    Shervin Mehryar
    Remzi Çelebi
    Christopher Brewster
- Ontology-based expansion of virtual gene panels to improve diagnostic efficiency for rare genetic diseases
  Pages
    87–91
  Authors
    Jae-Moon Shin
    Toyofumi Fujiwara
    Atsuko Yamaguchi
- Fine-Grained Named Entities for Corona News
  Pages
    92–97
  Authors
    Sefika Efeoglu
    Adrian Paschke
- Document-to-document relevance assessment for TREC Genomics Track 2005
  Pages
    98–101
  Authors
    Olga Giraldo
    María Fernanda Cadena
    Andrea Robayo-Gama
    Dhwani Solanki
    Tim Fellerhoff
    Lukas Geist
    Rohitha Ravinder
    Muhammad Talha
    Dietrich Rebholz-Schuhmann
    Leyla Jael Castro
- Decentralised semantics in distributed health data ecosystems: Harmonising quantitative data from medical devices for improved insights-driven applications
  Pages
    102–106
  Authors
    Paul Knowles
    Robert Mitwicki
    Michal Pietrus
- Surveyed common data access policies preferences amongst European Reference Networks
  Pages
    107–111
  Authors
    Alberto Cámara
    Nirupama Benis
    César H. Bernabé
    Inés de Oliveira Coelho
    Clémence M.A. Le Cornec
    Aylin Demir
    Bruna Dos Santos Vieira
    Jose Antonio Ramírez
    K. Joeri van der Velde
    Shuxin Zhang
    Ronald Cornet
    Annika Jacobsen
    Marco Roos
    Franz Schaefer
    Morris A. Swertz
    Mark D. Wilkinson

### Poster Papers

- Towards a Systems Pharmacology Ontology: the use of state-machines paradigm
  Pages
    112–113
  Authors
    Achilleas Chytas
    Nick Bassiliades
    Ioannis Vlahavas
    Pantelis Natsiavas
- The FAIR Data Point Populator: collaborative FAIRification and population of FAIR Data Points
  Pages
    114–115
  Authors
    Daphne Wijnbergen
    Rajaram Kaliyaperumal
    Marco Roos
    Eleni Mina
- Making expert curated knowledge graphs FAIR
  Pages
    116–117
  Authors
    Jerven Bolleman
    Alan Bridge
    Nicole Redaschi
    UniProt Consortium
- Towards the use of semantic rules to prioritize patient input requests in ePRO systems
  Pages
    118–119
  Authors
    Pantelis Natsiavas
    Panos Bonotis
- To build densely connected Web of RDF data
  Pages
    120–121
  Authors
    Yasunori Yamamoto
    Takatomo Fujisawa
- Contributions to the reuse and reproducibility of computational biology models
  Pages
    122–123
  Authors
    Ron Henkel
    Dagmar Waltemath
- Comparative analysis of protein function text-based embeddings and their applicability to prediction tasks
  Pages
    124–125
  Authors
    Rohitha Ravinder
    Leyla Jael Castro
    Martin Hofmann-Apitius
    Dietrich Rebholz-Schuhmann
- Genome Variation Ontology for annotation of complex structural variations
  Pages
    126–127
  Authors
    Shuichi Kawashima
    Takatomo Fujisawa
    Toshiaki Katayama
- Developing a semantic event search engine for biomedical events
  Pages
    128–129
  Authors
    Julio Cesar Rangel Reyes
    Norio Kobayashi
- FAIRification and semantic modelling for Duchenne and Becker Muscular Dystrophy rare diseases
  Pages
    130–132
  Authors
    Pablo Perdomo-Quinteiro
    Sergiu Siminiuc
    Paraskevi Sakellariou
    Marco Roos
    Pietro Spitali
    Núria Queralt-Rosinach
- MeDaX project plan: How to sustainably improve biomedical (research) data management
  Pages
    133–134
  Authors
    Judith A .H. Wodke
    Ron Henkel
    Dagmar Waltemath
- Towards Semantic Modeling of Patient Trajectories for Rehabilitation of Osteoarthritis
  Pages
    135–136
  Authors
    Gaetano Manzo
    Benjamin Pocklington
    Yvan Pannatier
    Cathy Gay
    Anjani Dhrangadhariya
    Sophie Carrard
    Roger Hilfiker
    Jean-Paul Calbimonte
- NFDI4BIOIMAGE: Perspective for a national bioimaging standard
  Pages
    137–138
  Authors
    Josh Moore
    Susanne Kunis
- First Steps Towards the FAIRification of the DZD CORE DATASET at the German Center for Diabetes Research
  Pages
    139–140
  Authors
    Esther Thea Inau
    Angela Dedie
    Ivona Anastasova
    Andreas Birkenfeld
    Brigitte Fröhlich
    Martin Hrabě de Angelis
    Michael Roden
    Renate Schick
    Yaroslav Zdravomyslov
    Atinkut Zeleke
    Dagmar Waltemath
    Martin Preusse
- An ontology for Age-Related Macular Degeneration using ophthalmologists and language models
  Pages
    141–142
  Authors
    Adrian Groza
    Anca Marginean
    Simona Delia Nicoara
- A Semantic Representation of the NFDI4Health Metadata Schema Utilizing the CEDAR Workbench
  Pages
    143–144
  Authors
    Matthias Löbe
    Aliaksandra Shutsko
    Carsten O. Schmidt
    Johannes Darms
    Sophie A. I. Klopfenstein
    Carina N. Vorisek
    Xioaming Hu
    Martin Golebiewski
    Juliane Fluck
- A metadata analysis for machine-actionable Software Management Plans
  Pages
    145–146
  Authors
    Olga Giraldo
    Renato Alves
    Dimitrios Bampalikis
    José M. Fernández
    Eva Martin del Pico
    Fotis Psomopoulos
    Nelson Quiñones
    Dhwani Solanki
    Allegra Via
    Leyla Jael Castro
- Structured review on Huntington's disease iron hypothesis
  Pages
    147–148
  Authors
    Karolis Cremers
    Marco Roos
    Katy Wolstencroft
    Eleni Mina
    Núria Queralt-Rosinach
- Text mining genome-wide association study literature
  Pages
    149–150
  Authors
    Thomas Rowlands
    Tim Beck
- Updating the CEMO ontology for future epidemiological challenges
  Pages
    151–152
  Authors
    Núria Queralt-Rosinach
    Paul N. Schofield
    Marco Roos
    Robert Hoehndorf
- Visualisation and Exploration of Linked Data Using Virtual Reality - a preview of Graph2VR
  Pages
    153–154
  Authors
    Alexander Kellmann
    Max Postema
    Joris de Keijser
    Pjotr Svetachov
    Becca Wilson
    Esther van Enckevort
    Morris A. Swertz
- Multilabel-classification task for Medline abstracts
  Pages
    155–156
  Authors
    Nelson Quiñones
    Cesar Canales
    Javier Torres
    Dietrich Rebholz-Schuhmann
    Leyla Jael Castro
    Andrés Aristizábal
- Experiences from compiling a FAIR survey in the German Network University Medicine
  Pages
    157–158
  Authors
    Lea Michaelis
    Rasim Atakan Poyraz
    Michael Rusongoza Muzoora
    Kerstin Gierend
    Alexander Bartschke
    Dagmar Waltemath
    Sylvia Thun
- OntoClue, a framework to compare vector-based approaches for document relatedness using the RELISH corpus
  Pages
    159–160
  Authors
    Rohitha Ravinder
    Tim Fellerhoff
    Vishnu Dadi
    Lukas Geist
    Guillermo Rocamora
    Muhammad Talha
    Dietrich Rebholz-Schuhmann
    Leyla Jael Castro
- Text-based phenotyping with Semantic Deep Learning: setting up experiments for women’s health
  Pages
    161–162
  Authors
    Mercedes Arguello Casteleiro
    Niamh Joyce
    Nava Maroto
    Maria Jesus Fernandez Prieto
    Tim Furmston
    Diego Maseda Fernandez
    Phillip Lord
    Chris Wroe
    John Keane
    Ying Cheong
    Robert Stevens
- An Explainable Intervention Prediction for Trauma Patients
  Pages
    163–164
  Authors
    Zoe Vasileiou
    Georgios Meditskos
    Stefanos Vrochidis
    Nick Bassiliades

### Demonstrations

- FHIR-Ontop-OMOP: Querying OMOP clinical databases as FHIR-compliant Clinical Knowledge Graphs
  Pages
    165–166
  Authors
    Guohui Xiao
    Emily Pfaff
    Eric Prud'Hommeaux
    David Booth
    Deepak K. Sharma
    Nan Huo
    Yue Yu
    Nansu Zong
    Kathryn J. Ruddy
    Christopher G. Chute
    Guoqian Jiang
- AgroLD: a Knowledge Graph for the Plant Sciences
  Pages
    167–168
  Authors
    Pierre Larmande
    Bertrand Pitollat
    Ndomassi Tando
    Yann Pomie
    Bill Happi
    Valentin Guignon
    Manuel Ruiz
- Analyze Decentralized Personal Health Data Using Solid, Digital Consent, and Federated Learning
  Pages
    169–170
  Authors
    Chang Sun
    Johan van Soest
    Michel Dumontier
- Managing food and microbiome studies data using Fairspace, a flexible and FAIR data management platform
  Pages
    171–172
  Authors
    Ewelina Grudzien
    Eelke van der Horst
    Frank van den Bergh
    Maria H. Traka
    Duncan Ng
    Falk Hildebrand
    Chris T. Evelo
    Susan L. M. Coort
    Duygu Dede Şener
    Elisa Cirillo

### Data-In-Use Papers

- Towards predicting essential proteins via federated SPARQL queries
  Pages
    173–174
  Authors
    Petros Liakopoulous
    Borbala Banfalvi
    Xinyi Wang
    Sina Majidian
    Tarcisio Mendes de Farias
    Christophe Dessimoz
    Ana Claudia Sima
- A federated query between neXtProt and OrthoDB retrieves 44 uncharacterized human proteins highly expressed in the brain and conserved in Drosophila melanogaster
  Pages
    175–176
  Authors
    Lydie Lane
    Kasun Samarasinghe
    Pierre-André Michel
- Data in use for Alzheimer disease study: combining gene expression, orthology, bioresource and disease datasets
  Pages
    177–178
  Authors
    Tarcisio Mendes de Farias
    Tatsuya Kushida
    Ana Claudia Sima
    Christophe Dessimoz
    Hirokazu Chiba
    Frédéric Bastian
    Hiroshi Masuya
- Linking glycan and protein data
  Pages
    179–180
  Authors
    Catherine Hayes
    Vincenzo Daponte
    Frederique Lisacek
- UniProt, ChEBI and IDSM Sachem: exploring biologically relevant ligands
  Pages
    181–183
  Authors
    Sebastien Gehant
    Elisabeth Coudert
    Anne Morgat
    Jerven Bolleman
    Nicole Redaschi
    Alan Bridge
    UniProt Consortium

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