Semantic Web Applications and Tools for Healthcare and Life Sciences

Scientific Programme 2022

Designed to accommodate hybrid attendance over different time-zones

 Conference Schedule 11-12 Jan 2022 – on site and online

Day 1 – Morning Session

09:30-10:00 Registration/login

10:00 – 10:15 welcome and introduction

10:15- 11:00 Keynote: Prof Mirjam van Reisen

11:00-11:30 coffee

11:30-12:30  Presentation session 1

12:30 – 13:15  Lightning poster and demo presentations

13:15 -14:30 Lunch Break

14:30-15:30 online poster and demo session in Gathertown


Afternoon Session

15:30 – 16:30 Presentation session 2

16:30-17:15  Round table discussion on selected papers/posters

17:15- 17:45 coffee and physical poster session

17:45 – 18:45 Panel session – Agrisemantics,

18:45 – 19:30 Keynote 2: Prof Karin Verspoor


Day 2 – Morning Session

09:30-10:00 Registration

10:00 –11:00 presentation session 3

11:00-11:30 coffee

11:30-12:15  Keynote – Dr Martina Summer-Kutmon

12:15 – 13:00  round table on selected papers/posters

13:00 – 15:30 Lunch and social Event in Leiden for physical participants

13:30 – 15:30 Optional Birds Of a Feather meetings online

Afternoon Session

15:30 – 16:30 Presentation session 4

16:30-18:45 Panel Session

18:45 – 19:30 Keynote: Professor Amit Sheth

19 :30-19 :45 Closing remarks and announcement of next SWAT4HCLS


Accepted Papers

  • Alasdair Gray, Petros Papadopoulos, Ivan Mičetić and András Hatos, Creating and Exploiting the Intrinsically Disordered Protein Knowledge Graph (IDP-KG)
  • Sabine Oesterle, Vasundra Touré and Katrin Crameri, The SPHN Ecosystem towards FAIR Data
  • Julie Loesch, Louis Meeckers, Ilse van Lier, Alie de Boer, Michel Dumontier and Remzi Celebi, Automated Identification of Food Substitutions Using Knowledge Graph Embeddings
  • Rajaram Kaliyaperumal, Gurnoor Singh, Núria Queralt-Rosinach, Jumamurat Bayjanov, Peter-Bram T Hoen and Marco Roos, Phenopackets for the Semantic Web
  • César Bernabé, Núria Queralt-Rosinach, Vitor Souza, Luiz Santos, Annika Jacobsen, Barend Mons and Marco Roos, The use of Foundational Ontologies in Bioinformatics
  • Chang Sun, Vincent Emonet and Michel Dumontier, A comprehensive comparison of automated FAIRness Evaluation Tools
  • Olga Giraldo, Miguel Ruano, Robin A. Richardson, Remzi Celebi, Michel Dumontier and Tobias Kuhn, Nanotate: Semantically annotating experimental protocols with nanopublications,
  • Vincenzo Daponte, Catherine Hayes, Julien Mariethoz and Frederique Lisacek, Glycan semantic model applications in substructure search
  • Deepak Sharma, Eric Prud’hommeaux, David Booth, Kevin Peterson, Daniel Stone, Harold Solbrig, Guohui Xiao, Emily Pfaff and Guoqian Jiang, Implementing a New FHIR RDF Specification for Semantic Clinical Data Using a JSON-LD-based Approach
  • Frances Gillis-Webber and C. Maria Keet, A Survey of Multilingual OWL Ontologies in BioPortal
  • Ali Syed, Senay Kafkas, Maxat Kulmanov and Robert Hoehndorf, Using SPARQL to unify queries over data, ontologies, and machine learning models in the PhenomeBrowser knowledgebase
  • Helena Balabin, Charles Hoyt, Benjamin M. Gyori, John Bachman, Alpha Tom Kodamullil, Martin Hofmann-Apitius and Daniel Domingo-Fernández, ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs
  • 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 and Chris Wroe, MetaMap versus BERT models with explainable active learning: ontology-based experiments with prior knowledge for COVID-19
  • Fuqi Xu, Nick Juty, Carole Goble, Simon Jupp, Helen Parkinson and Mélanie Courtot, Features of a FAIR vocabulary
  • Ruduan Plug, Yan Liang, Mariam Basajja, Aliya Aktau, Putu Jati, Samson Amare, Getu Taye, Mouhamad Mpezamihigo, Francisca Oladipo and Mirjam van Reisen: FAIR and GDPR Compliant Population Health Data Generation, Processing and Analytics


Accepted Posters and Demos

  • Achilleas Chytas, Anargyros Kapetanakis, Giorgos Gavriilidis, Marie-Christine Jaulent and Pantelis Natsiavas, OpenPVSignal: Quality Assurance when building a Knowledge Graph for Pharmacovigilance Signal Reports
  • Sumyyah Toonsi, Şenay Kafkas and Robert Hoehndorf, An ontology-based semi-supervised method for concept recognition in biomedical text
  • Jasper Koehorst, Bart Nijsse and Peter Schaap, UNLOCK a FAIR by Design large-scale national infrastructure for research on microbial communities.
  • Fernando Zhapa-Camacho, Sarah Alghamdi, Azza Althagafi, Sara Althubaiti, Sumyyah Toonsi, Maxat Kulmanov and Robert Hoehndorf, GNN-Sim: Trainable semantic similarity over biomedical ontologies using graph neural networks
  • Petros Kalendralis, Matthijs Sloep, Jasper Snel, Nibin Moni George, Joeri Veugen, Johan van Soest, Andre Dekker and Rianne Fijten, A knowledge graph based on the proton therapy model based approach for head and neck patients.
  • Koen Haverkort, Vedran Kasalica and Anna-Lena Lamprecht, APE Web: A Web Interface for Automated Workflow Exploration with APE
  • Ammar Ammar, Chris Evelo and Egon Willighagen, NSDRA: unifying 281 FAIR maturity indicators from 12 minimum reporting standards for nanosafety
  • Ammar Ammar, Marvin Martens, Jeaphianne P.M. van Rijn, Denise N. Slenter, Laurent Winckers, Chris T. Evelo and Egon L. Willighagen, Semantic web applications and tools developed and deployed by BiGCaT
  • Marvin Martens, Chris Evelo and Egon Willighagen, Semantic modelling of Adverse Outcome Pathways and the implementation in reproducible workflows
  • Yi Chen, Katherine Wolstencroft and Frank Takes, The Impact of Gene Ontology Evolution on the Comparability of Omics Results
  • Jeaphianne van Rijn, Marvin Martens, Ammar Ammar and Egon Willighagen, Exploring Adverse Outcome Pathways for nanomaterials with semantic web technologies
  • Matthijs Sloep, Petros Kalendralis, Jasper Snel, Nibin Moni George, Andre Dekker, Johan van Soest and Rianne Fijten, Federated analysis of observational patient data in Dutch radiotherapy centres
  • Ammar Ammar, Marvin Martens, Jeaphianne P.M. van Rijn, Denise N. Slenter, Laurent Winckers, Chris T. Evelo and Egon L. Willighagen: Semantic web applications and tools developed and deployed by BiGCaT
  • Julio Cesar Rangel Rangel and Norio Kobayashi: A trial implementation of entity linking connecting life-science documents and ontologies