Mon 13 Feb – Tutorials day
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 |
Keynote |
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 |
|
| 11:00-11:30 | Coffee Break | ||
| 11:30-12 | KG Applications
Chair: Andra Waagmeester Q&A: Discord #kg-application |
Paper |
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‡ |
|
| 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 | ||
| 15:00-15:30 |
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 |
| 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 | ||
| 9:00-10:00 |
Data Modeling Chair: Jerven Bolleman |
Keynote |
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‡ |
|
| 11:00-11:30 | Coffee Break | ||
| 11:30-12 |
NLP Chair: Atsuko Yamaguchi |
Paper |
Lorcán Pigott-Dix‡ and Robert P. Davey |
| 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 |
|
| 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 | ||
| 14:00-14:30 |
Data Sharing & Integration Chair: Leyla Jael Castro |
Paper |
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 |
|
| 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) |
Thu 16 Feb – Hackathon day
Posters, demos, data papers
Demos
- 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)
Data
- 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
Panellists:
Leyla Jael Castro (ZB MED, NFDI4DataScience, Bioschemas)
Saritha Kuriakose (Novo Nordisk)
Erick Antezana (Bayer Cropscience)
Josh Moore (German Bioimaging, NFDI4BIOIMAGE)
Rajaram Kaliyaperumal(J&J)