Swat4ls Conference in Basel, 13-16 Feb 2023

Scientific Programme 2023


Mon 13 Feb – Tutorials day

Tutorials running on parallel tracks all day (9-17 CET).
Detailed program and recordings on the tutorials page.

Tue 14-15 Feb – SWAT4LS conference

Tuesday 14th (all times in CET)

‡Author that presented live.

Click on the titles to watch the recording.
You can also watch the unedited full stream of the Tuesday 14th

8:30-9:00   Wellcome coffee  
9:00-10:00 Healthcare

Chair: Sabine Österle

Q&A: Discord #healthcare


Katrin Crameri‡

The Swiss Personalized Health Network – FAIRification of health data

10:00-10:30 Paper

Gerhard Kober‡, Adrian Paschke and Livio Robaldo

Using BPMN for medical guidelines that integrate with FHIR-RDF

10:30-11 Paper

Varsha Gouthamchand‡, Andre Dekker, Johan Van Soest and Leonard Wee

Privacy-Preserving Dashboard for F.A.I.R Head and Neck Cancer data supporting multi-centered collaborations

11:00-11:30   Coffee Break  
11:30-12 KG Applications

Chair: Andra Waagmeester

Q&A: Discord #kg-application


Elif Ozkan, Remzi Celebi, Arif Yilmaz‡, Vincent Emonet and Michel Dumontier‡

Generating Knowledge Graph Based Explanations for Drug Repurposing Predictions

12:00-12:15 Short paper

Özge Erten‡, Shervin Mehryar‡, Remzi Çelebi and Christopher Brewster

Predicting missing annotations in Gene Ontology with Knowledge Graph Embeddings and True Path Rule

12:15-12:30 Short paper

Jae-Moon Shin, Toyofumi Fujiwara and Atsuko Yamaguchi‡

Ontology-based expansion of virtual gene panels to improve diagnostic efficiency for rare genetic diseases

12:20-13:15   Lunch  
13:15-14:00   Poster flash 1-min flash presentations: 26 posters, 5 data, 4 demos
14:00-15:00   Poster Session & Coffee Break  

Chair: Ole Eigenbrod

Industry session

Industry talk (R)

Elizabeth Hanson (Benchsci)

Enriching the Biological Knowledge Graph with Ontological Data

15:30-16:00 Industry talk

Erick Antezana‡ (Bayer Cropscience)

Linked Data experiences

16:00-16:30 Industry talk Saritha Kuriakose (Novo Nordisk)
16:30-17:00 Sponsored talk

Todor Primov‡

Ontotext Knowledge Graph Powered Target Discovery Solution

Ontotext’s Knowledge Graph powered Target Discovery helps biotechnology & Pharma companies identify new drug targets and promising drug repurposing candidates quickly, efficiently and with confidence. Relevant data sources are mapped and managed in a central Knowledge Graph, allowing expert users to extract valuable facts about any entity & context of interest, be it gene, disease or protein, in a matter of seconds. Customizable algorithmic & visual analytics are layered on top of the data to facilitate in-depth insights, validate scientific hypothesis, and drive data-driven decision making in target assessment and prioritization, resulting in an increased number of potential targets in the pipeline

17:00-18:00 Chair: M. Scott Marshall Keynote (R)

Ora Lassila

Reimagining the Semantic Web – a retrospective

18:00-18:30   move to dinner  
18:30-23:00   Apero & Dinner  

Wednesday 15th, (all times in CET)

‡Author that will be presented live.

Click on the titles to watch the recording.
You can also watch the unedited full stream of the Wednesday 15th

8:30-9:00   Wellcome coffee  

Data Modeling

Chair: Jerven Bolleman


Chris Mungall‡

Scaling up semantics: lessons learned from across the life sciences

10:00-10:30 Paper

Qingliang Li, Sunghwan Kim, Leonid Zaslavsky, Tiejun Cheng, Bo Yu and Evan Bolton‡

RDF modeling of the co-occurrences of named entities derived from biomedical literature in PubChem

10:30-11 Paper

Arif Yilmaz‡, Raghavendra Naidu and Christopher Brewster‡

FSO: Food Safety Monitoring Ontology

11:00-11:30   Coffee Break  


Chair: Atsuko Yamaguchi


Lorcán Pigott-Dix‡ and Robert P. Davey

Attention for Multi-Ontology Concept Recognition

12:00-12:30 Paper (R)

Nora Abdelmageed‡, Felicitas Löffler and Birgitta König-Ries

BiodivBERT: a Pre-Trained Language Model for the Biodiversity Domain

12:30-12:45 Short paper

Sefika Efeoglu‡ and Adrian Paschke

Fine-Grained Named Entities for Corona News

12:45-13:00 Short paper

Olga Giraldo, María Fernanda Cadena, Andrea Robayo-Gama, Dhwani Solanki‡, Tim Fellerhoff, Lukas Geist, Rohitha Ravinder, Muhammad Talha, Dietrich Rebholz-Schuhmann and Leyla Jael Castro‡

Document-to-document relevance assessment for TREC Genomics Track 2005

13:00-14:00   Lunch  

Data Sharing & Integration

Chair: Leyla Jael Castro


Yi Chen‡, Fons.J Verbeek and Katherine Wolstencroft

FAIR Functional Enrichment: Assessing and Modelling Provenance in Omics Results

14:30-14:45 Short paper

Paul Knowles‡ and Robert Mitwicki

Decentralised semantics in distributed health data ecosystems: Harmonising electronic health data from medical devices for improved insights-driven applications

14:45-15:00 Short paper

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 and Mark D. Wilkinson

Common data access policies amongst European Reference Networks

15:00-16:00   Coffee Break Last hour to vote on posters.
16:00-17:00   Keynote

Frank van Harmelen‡

Combining knowledge graphs with machine learning, with examples from healthcare and life sciences.

17:00-18:00 Chair: Andra Waagmeester Panel

Performers staring at the sparqling semantic stars from the earth (Leyla Jael Castro, Saritha Kuriakose, Erick Antezana, Josh Moore, Rajaram Kaliyaperumal) 
Panel discussion and closing

Thu 16 Feb – Hackathon day

Self organising Hackathon running on multiple tracks
Look for BIOHACKATHON SWAT4HCLS category on Discord.

Posters, demos, data papers


  • FHIR-Ontop-OMOP: Querying OMOP clinical databases as FHIR-compliant Clinical Knowledge Graphs (Guohui Xiao, Emily Pfaff, Eric Prud’Hommeaux, David Booth, Deepak K. Sharma, Nan Huo, Yue Yu, Nansu Zong, Kathryn J. Ruddy, Christopher G. Chute and Guoqian Jiang)
  • AgroLD: a Knowledge Graph for the Plant Sciences (Pierre Larmande, Bertrand Pitollat, Ndomassi Tando, Yann Pomie, Bill Happi, Valentin Guignon and Manuel Ruiz)
  • Analyze Decentralized Personal Health Data Using Solid, Digital Consent, and Federated Learning (Chang Sun, Johan van Soest and Michel Dumontier)
  • Managing food and microbiome studies data using Fairspace, a flexible and FAIR data management platform (Ewelina Grudzien, Eelke van der Horst, Frank van den Bergh, Maria Traka, Duncan Ng, Falk Hildebrand, Chris Evelo, Susan Coort, Duygu Sener and Elisa Cirillo)


  • Towards predicting essential proteins via federated SPARQL queries (Petros Liakopoulous, Borbala Banfalvi, Xinyi Wang, Sina Majidian, Tarcisio Mendes de Farias, Christophe Dessimoz and 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. (Lydie Lane, Kasun Samarasinghe and Pierre-André Michel)
  • Data in use for Alzheimer disease study: combining gene expression, orthology, bioresource and disease datasets (Tarcisio Mendes de Farias, Tatsuya Kushida, Ana Claudia Sima, Christophe Dessimoz, Hirokazu Chiba, Frederic Bastian and Hiroshi Masuya)
  • Linking glycan and protein data (Catherine Hayes, Vincenzo Daponte, Julien Mariethoz and Frederique Lisacek)

Posters (confirmed)

  • (P-1) Towards a Systems Pharmacology Ontology: the use of state-machines paradigm (Achilleas Chytas, Nick Bassiliades, Ioannis Vlahavas and Pantelis Natsiavas)
  • (P-2) The FAIR Data Point Populator: collaborative FAIRification and population of FAIR Data Points (Daphne Wijnbergen, Rajaram Kaliyaperumal, Marco Roos and Eleni Mina)
  • (P-3) Making expert-curated knowledge graphs FAIR (Jerven Bolleman, Alan Bridge and Nicole Redaschi)
  • (P-4) Towards the use of semantic rules to prioritize patient input requests in ePRO systems (Pantelis Natsiavas and Panos Bonotis)
  • (P-5) To build a densely connected Web of RDF data (Yasunori Yamamoto and Takatomo Fujisawa)
  • (P-6) Contributions to the reuse and reproducibility of computational biology models (Ron Henkel)
  • (P-7) Comparative analysis of protein function text-based embeddings and their applicability to prediction tasks (Rohitha Ravinder, Leyla Jael Castro, Martin Hofmann-Apitius and Dietrich Rebholz-Schuhmann)
  • (P-8) Genome Variation Ontology for annotation of complex structural variations (Shuichi Kawashima, Takatomo Fujisawa and Toshiaki Katayama)
  • (P-9) Developing a semantic event search engine for biomedical events (Julio Cesar Rangel Reyes and Norio Kobayashi)
  • (P-10) FAIRification and semantic modelling for Duchenne and Becker Muscular Dystrophy rare diseases (Pablo Perdomo-Quinteiro, Sergiu Siminiuc, Elvina Sakellariou, Marco Roos, Pietro Spitali and Núria Queralt-Rosinach)
  • (P-11) MeDaX project plan: How to sustainably improve biomedical (research) data management (Judith A.H. Wodke, Ron Henkel and Dagmar Waltemath)
  • (P-12) Towards Semantic Modeling of Patient Trajectories for Rehabilitation of Osteoarthritis (Gaetano Manzo, Benjamin Pocklington, Yvan Pannatier, Cathy Gay, Anjani Dhrangadhariya, Sophie Carrard, Roger Hilfiker and Jean-Paul Calbimonte)
  • (P-13) NFDI4BIOIMAGE: Perspective for a national bioimaging standard (Josh Moore and Susanne Kunis)
  • (P-14) First Steps Towards the FAIRification of the DZD CORE DATASET at the German Center for Diabetes Research (Esther Inau, Angela Dedie, Ivona Anastasova, Andreas Birkenfeld, Brigitte Fröhlich, Martin Hrabe de Angelis, Michael Roden, Renate Schick, Yaroslav Zdravomyslov, Atinkut Zeleke, Dagmar Waltemath and Martin Preusse)
  • (P-15) An ontology for Age-Related Macular Degeneration using ophthalmologists and language models (Adrian Groza, Anca Marginean and Simona Delia Nicoara)
  • (P-16) A Semantic Representation of the NFDI4Health Metadata Schema Utilizing the CEDAR Workbench (Matthias Löbe, Aliaksandra Shutsko, Carsten Schmidt, Johannes Darms, Sophie Klopfenstein, Carina Vorisek, Xioaming Hu, Martin Golebiewski and Juliane Fluck)
  • (P-17) A metadata analysis for machine-actionable Software Management Plans (Olga Giraldo, Renato Alves, Dimitrios Bampalikis, José M. Fernández, Eva Martin del Pico, Fotis Psomopoulos, Nelson Quiñones, Dhwani Solanki, Allegra Via and Leyla Jael Castro)
  • (P-18) Structured review on Huntington’s disease iron hypothesis (Karolis Cremers, Marco Roos, Katy Wolstencroft, Eleni Mina and Núria Queralt-Rosinach)
  • (P-19)Text mining genome-wide association study literature (Thomas Rowlands and Tim Beck)
  • (P-20) Updating the CEMO ontology for future epidemiological challenges (Núria Queralt Rosinach, Paul N. Schofield, Marco Roos and Robert Hoehndorf)
  • (P-21) Text-based phenotyping with Semantic Deep Learning: setting up experiments for women’s health (M Arguello-Casteleiro, N Joyce, N Maroto, Mj Fernandez-Prieto, T Furmston, D Maseda Fernandez, P Lord, C Wroe, J Keane, Y Cheong and R Stevens)
  • (P-22) Multilabel-classification task for Medline abstracts (Nelson Quiñones, César Canales, Javier Torres, Dietrich Rebholz-Schuhmann, Leyla Jael Castro and Andrés Aristizábal)
  • (P-23) Experiences from compiling a FAIR survey in the German Network University Medicine (Lea Michaelis, Rasim Atakan Poyraz, Michael Rusongoza Muzoora, Alexander Bartschke, Kerstin Gierend, Dagmar Waltemath and Sylvia Thun)
  • (P-24) A comparison on vector-based approaches for document similarity in the RELISH corpus (Rohitha Ravinder, Tim Fellerhoff, Vishnu Dadi, Lukas Geist, Guillermo Rocamora, Muhammad Talha, Dietrich Rebholz-Schuhmann and Leyla Jael Castro)
  • (P-25) tol-KG: A framework to integrate tolDC data using Linked Knowledge Graphs and Machine Learning (Ayesha Sahar, Michael Hughes, Lee Harland, Catharien Hilkens and Phillip Lord)
  • (PV-1) Text-based phenotyping with Semantic Deep Learning: setting up experiments for women’s health (M Arguello-Casteleiro, N Joyce, N Maroto, Mj Fernandez-Prieto, T Furmston, D Maseda Fernandez, P Lord, C Wroe, J Keane, Y Cheong and R Stevens)
  • (PV-2) An Explainable Intervention Prediction for Trauma Patients (Zoe Vasileiou, Georgios Meditskos, Stefanos Vrochidis and Nick Bassiliades)

Panel discussion: Performers staring at the sparqling semantic stars from the earth

Leyla Jael Castro (ZB MED, NFDI4DataScience, Bioschemas)

Saritha Kuriakose (Novo Nordisk)

Erick Antezana (Bayer Cropscience)

Josh Moore (German Bioimaging, NFDI4BIOIMAGE)

Rajaram Kaliyaperumal(J&J)