# SWAT4HCLS 2022 Semantic Web Applications and Tools for Health Care and Life Sciences

Event
  13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences
Location
  Virtual Event, Leiden, Netherlands
Date
  January 10th to 14th, 2022

Edited by
  Katy Wolstencroft1
  Andrea Splendiani2
  M. Scott Marshall3
  Chris Baker4
  Andra Waagmeester5
  Marco Roos6
  Rutger Vos7
  Rianne Fijten8
  Leyla Jael Castro9

- 1LIACS, Leiden University, The Netherlands
- 2Novartis, Switzerland
- 3Annalect, The Netherlands
- 4University of New Brunswick, Canada
- 5Micelio, Antwerp, Belgium
- 6Leiden University Medical Centre, The Netherlands
- 7Naturalis, The Netherlands
- 8Maastro, The Netherlands
- 9ZB MED, Germany

## Table of Contents

1. Preface

   Summary: There were 26 papers submitted for peer-review to this workshop. Out of these, 15 papers were accepted for this volume.

2. Creating and Exploiting the Intrinsically Disordered Protein Knowledge Graph (IDP-KG)
   Pages
     1–10
   Authors
     Alasdair J. G. Gray
     Petros Papadopoulos
     Imran Asif
     Ivan Mičetić
     András Hatos
3. The SPHN Ecosystem towards FAIR Data
   Pages
     11–18
   Authors
     Sabine Österle
     Vasundra Touré
     Katrin Crameri
4. Automated Identification of Food Substitutions Using Knowledge Graph Embeddings
   Pages
     19–28
   Authors
     Julie Loesch
     Louis Meeckers
     Ilse van Lier
     Alie de Boer
     Michel Dumontier
     Remzi Celebi
5. Phenopackets for the Semantic Web
   Pages
     29–33
   Authors
     Rajaram Kaliyaperumal
     Gurnoor Singh
     Núria Queralt-Rosinach
     Jumamurat Bayjanov
     Peter-Bram 't Hoen
     Marco Roos
6. The Use of Foundational Ontologies in Bioinformatics
   Pages
     34–43
   Authors
     César Henrique Bernabé
     Núria Queralt-Rosinach
     Vítor E. Silva Souza
     Luiz Olavo Bonino da Silva Santos
     Annika Jacobsen
     Barend Mons
     Marco Roos
7. A Comprehensive Comparison of Automated FAIRness Evaluation Tools
   Pages
     44–53
   Authors
     Chang Sun
     Vincent Emonet
     Michel Dumontier
8. FAIR and GDPR Compliant Population Health Data Generation, Processing and Analytics
   Pages
     54–63
   Authors
     Ruduan Plug
     Yan Liang
     Mariam Basajja
     Aliya Aktau
     Putu Hadi Purnama Jati
     Samson Yohannes Amare
     Getu Tadele Taye
     Mouhamad Mpezamihigo
     Francisca Oladipo
     Mirjam van Reisen
9. Nanotate: Semantically Annotating Experimental Protocols with Nanopublications
   Pages
     64–73
   Authors
     Olga Giraldo
     Miguel Ruano
     Robin A. Richardson
     Remzi Celebi
     Michel Dumontier
     Tobias Kuhn
10. Glycan Semantic Model Applications in Substructure Search
    Pages
      74–81
    Authors
      Vincenzo Daponte
      Catherine Hayes
      Julien Mariethoz
      Frederique Lisacek
11. Implementing a New FHIR RDF Specification for Semantic Clinical Data Using a JSON-LD-based Approach
    Pages
      82–86
    Authors
      Deepak K. Sharma
      Eric Prud’hommeaux
      David Booth
      Kevin J. Peterson
      Daniel J. Stone
      Harold Solbrig
      Guohui Xiao
      Emily Pfaff
      Guoqian Jiang
12. A Survey of Multilingual OWL Ontologies in BioPortal
    Pages
      87–96
    Authors
      Frances Gillis-Webber
      C. Maria Keet
13. Using SPARQL to Unify Queries over Data, Ontologies, and Machine Learning Models in the PhenomeBrowser Knowledgebase
    Pages
      97–102
    Authors
      Ali Syed
      Şenay Kafkas
      Maxat Kulmanov
      Robert Hoehndorf
14. ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs
    Pages
      103–107
    Authors
      Helena Balabin
      Charles Tapley Hoyt
      Benjamin M. Gyori
      John Bachman
      Alpha Tom Kodamullil
      Martin Hofmann-Apitius
      Daniel Domingo-Fernández
15. MetaMap versus BERT Models with Explainable Active Learning: Ontology-Based Experiments with Prior Knowledge for COVID-19
    Pages
      108–117
    Authors
      Mercedes Arguello-Casteleiro
      Chloe Henson
      Nava Maroto
      Saihong Li
      Julio Des-Diz
      Maria Jesus Fernandez-Prieto
      Simon Peters
      Timothy Furmston
      Carlos Sevillano-Torrado
      Diego Maseda-Fernandez
      Manoj Kulshrestha
      John Keane
      Robert Stevens
      Chris Wroe
16. Features of a FAIR Vocabulary
    Pages
      118–148
    Authors
      Fuqi Xu
      Nick Juty
      Carole Goble
      Simon Jupp
      Helen Parkinson
      Mélanie Courtot

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