Semantic Web Applications and Tools for Healthcare and Life Sciences
SWAT4HCLS 2022

Scientific Programme 2022

Designed to accommodate online attendance over different time-zones

 Conference Schedule 11-12 Jan 2022 – online

Day 1 Tue 11 Jan– Morning Session
09:00 – 09:30    Registration / login
09:30 – 09:45    Welcome and introduction – Marco Roos and Katy Wolstencroft
09:45 – 10:30    Keynote: Prof Karin Verspoor – Chair: Marco Roos
10:30 – 10:50    Coffee break
10:50 – 12:30    Presentations: Semantic Web and FAIR Health – Chair: Rianne Fijten

10:50-11:10

Sabine Oesterle, Vasundra Touré and Katrin Crameri, The SPHN Ecosystem towards FAIR Data

11:15-11:35

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

11:40-12:00

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

12:00-12:20

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

12:25 – 13:30    Lunch
13:30 – 14:00    Online poster pitches for Posters in Group 1, Chair Andrea Splendiani

14:00-15:00 Gathertown Poster Session

Afternoon Session
15:00 – 15:45   Keynote: Dr. Martina Summer-Kutmon – Chair Andra Waagmeester

15:50 – 16:20 Invited Talk – FAIR Agronomy where are we, The KnetMiner Use Case, Marco Brandizi and Keywan Hassani-Pak, Introduced by Chris Baker
16:20-16:45 Coffee Break

Online Evening Session
16:45 – 18:20  Presentation session 2 – Knowledge Graphs Chair: M. Scott Marshall

16:45 – 17:05

Alasdair Gray, Petros Papadopoulos, Ivan Mičetić and András Hatos, Creating and Exploiting the Intrinsically Disordered Protein Knowledge Graph (IDP-KG)

17:10-17:30

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

17:35-17:55

Vincenzo Daponte, Catherine Hayes, Julien Mariethoz and Frederique Lisacek, Glycan semantic model applications in substructure search

18:00-18:20

Julie Loesch, Louis Meeckers, Ilse van Lier, Alie de Boer, Michel Dumontier and Remzi Celebi, Automated Identification of Food Substitutions Using Knowledge Graph Embeddings

18:20-18:30    Comfort break
18:30 – 19:30   Panel session – Agri-semantics. Chair Chris Baker

Day 2 Wed 12 Jan – Morning Session
09:00 – 09:30    Registration / login
09:30 – 11:00    Presentations 3 Ontologies, Semantic Annotation and FAIR Standards, Chair: Leyla Jael Garcia Castro

09:30-09:50

Chang Sun, Vincent Emonet and Michel Dumontier, A comprehensive comparison of automated FAIRness Evaluation Tools

09:55-10:15

Fuqi Xu, Nick Juty, Carole Goble, Simon Jupp, Helen Parkinson and Mélanie Courtot, Features of a FAIR vocabulary

10:20-10:40

Olga Giraldo, Miguel Ruano, Robin A. Richardson, Remzi Celebi, Michel Dumontier and Tobias Kuhn, Nanotate: Semantically annotating experimental protocols with nanopublications

10:45-11:05

Frances Gillis-Webber and C. Maria Keet, A Survey of Multilingual OWL Ontologies in BioPortal

11:05 – 11:30    Coffee break
11:30 – 12:15    Keynote: Prof Mirjam van Reisen. Chair Katy Wolstencroft

 12:15 – 13:15    Lunch break

13:15 – 13:45 Online poster pitches group 2

13:45-14:45 Gathertown Poster Session

14:45-15:00 Short break

Afternoon Session
15:00-16:10    Presentations session 4 – Chair Rutger Vos

15:00-15:20

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

15:25-15:45

Rajaram Kaliyaperumal, Gurnoor Singh, Núria Queralt-Rosinach, Jumamurat Bayjanov, Peter-Bram T Hoen and Marco Roos, Phenopackets for the Semantic Web

15:50-16:10

César Bernabé, Núria Queralt-Rosinach, Vitor Souza, Luiz Santos, Annika Jacobsen, Barend Mons and Marco Roos, The use of Foundational Ontologies in Bioinformatics

16:10-16:45     Coffee break

16:45 – 17:30    Keynote 4: Prof Amit Sheth – Chair: Chris Baker
17:30 – 17:50    Closing remarks and 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
  • Julio Cesar Rangel and Norio Kobayashi: A trial implementation of entity linking connecting life-science documents and ontologies
  • Anna Bernasconi, Ruba Al Khalaf, Tommaso Alfonsi, Arif Canakoglu, Luca Cilibrasi, Andrea Gulino, Pietro Pinoli and Stefano Ceri A unique approach to SARS-CoV-2 data and knowledge ingestion, integration and querying
  • Bruce Schultz and Christian Ebeling, e(BE:L): a framework for the enrichment and generation of multimodal knowledge graphs
  • Bernd Müller, Leyla Jael Castro and Dietrich Rebholz-Schuhmann, Merging Ontological Concepts by Lexical Features with a Focus on Pharmaceutical Compounds.
  • Sara Diaz Benavides, Silvio Cardoso, Marcos Da Silveira and Cédric Pruski, Comparing Versions of Ontologies and Understanding their Changes
  • Johann Frei and Frank Kramer, GERNERMED – An Open German Medical NER Model
  • Claudio Carta, Bruna Dos Santos Vieira, Rajaram Kaliyaperumal, Martijn G. Kersloot, Annika Jacobsen, Ronald Cornet, Mark D. Wilkinson, Marc Hanauer, Nirupama Benis, Laura L. Cellai, César H. Bernabé, Domenica Taruscio and Marco Roos, The 1st online Edition of the FAIR Data Game during the International Summer School on Rare Disease Registries & FAIRification of Data in Rome
  • Joeri van der Velde, Gurnoor Singh and Morris Swertz, FAIR Genomes: community development of guidelines, schema & systems for reuse of NGS data