Semantic Web Applications and Tools for Healthcare and Life Sciences

Accepted Papers and Posters


  • 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


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