swat4hcls 2019 Edinburgh


December 9th – Tutorials

8.30-9.00: coffee

9.00-11.00: Tutorials part 1

11.00-11.30: coffee

11.30-13.00: Tutorials part 2

13.00-14.00: lunch

14.00-15.30: Tutorials part 1 / 3

15.30-16.00 coffee

16.00-18.00: Tutorials part 2 / 4

Full day (9:00-18:00):

  • Querying SIB Swiss Institute of Bioinformatics resources with SPARQL (Jerven Bolleman, Dmitry Kuznetsov, Thierry Lombardot, Julien Mariethoz, Tarcisio Mendes, Marco Pagni, Monique Zahn/Lydie Lane) – Postgraduate Centre Room 201

Morning (9:00-13:00):

  • Creating a federated linked data landscape with Wikidata and Wikibase (Andra Waagmeester) – Postgraduate Centre Room 304
  • FHIR on Solid is FAIR (Eric Prud’hommeaux) – Postgraduate Centre Room 202

Afternoon (14:00-18:00):

December 10th – Conference Day 1 – The CAIRN Auditorium

8.30-9.00 Registration
9.00-9.15 Welcome, introduction.

  • Welcome from local organizer, Albert Burger
  • Welcome to SWAT4HCLS2019, Ronald Cornet
  • Introduction of keynote speaker
9.15-10.00 Keynote by Denny Vrandečić‎ 
Wikidata and beyond – Knowledge for everyone by everyone
10.00-10.40 Presentations, chaired by Ronald Cornet

  • Enhancing the maintainability of the Bio2RDF project using declarative mappings (Ana Iglesias-Molina, David Chaves-Fraga, Freddy Priyatna and Oscar Corcho)
  • Suggesting Reasonable Phenotypes to Clinicians (Laura Slaughter and Dag Hovland)
10.40-11.10 Coffee break
11.10-12.30 Presentations, chaired by Scott Marshall

  • A FHIR-to-RDF converter (Gerhard Kober and Adrian Paschke)
  • A framework for representing clinical research in FHIR (Hugo Leroux, Christine Denney, Smita Hastak and Hugh Glover)
  • Reconciling author names in taxonomic and publication databases (Roderic Page)
  • On Bringing Bioimaging Data into the Open(-World) (Josh Moore, Norio Kobayashi, Susanne Kunis, Shuichi Onami and Jason R. Swedlow)
12.30-13.30 Lunch break
13.30-14.15 Keynote by Birgitta König-Ries, introduced by Scott Marshall
Semantics for FAIR research data management
14.20-14.50 Lightning poster & demo presentations, chaired by Andra Waagmeester:

  • Realizing FAIR Data in an Enterprise Environment (Melanie Hackl and Goekhan Cosku)
  • Mapping subjects and domains across the humanities and natural sciences in FAIRsharing (Allyson Lister, Peter McQuilton, Milo Thurston and Susanna-Assunta Sansone)
  • Implementing FAIR Principles in InterMine (Daniela Butano, Justin Clark-Casey, Sergio Contrino, Josh Heimbach, Rachel Lyne, Kevin Herald Reierskog, Julie Sullivan, Yo Yehudi and Gos Micklem)
  • Publishing linked and FAIR-compliant radiomics data in radiation oncology via ontologies and Semantic Web techniques (Alberto Traverso, Martin Vallieres, Johan van Soest, Leonard Wee, Olivier Morin and Andre Dekker)
  • A modular approach to knowledge graphs and FAIR data in healthcare (Matthijs Sloep, Petros Kalendralis, Johan van Soest, Rianne Fijten and André Dekker)
  • MOLGENIS catalogue – towards a unified application for data and sample catalogues (Alexander Kellmann, David van Enckevort, Marije van der Geest, Aneas Hodselmans and Morris Swertz)
  • Semi-Automated Data-Driven Methods to Support Ontology Development: A Case Study on a Rehabilitation Therapy Ontology (Mohammad K. Halawani, Phillip Lord and Rob Forsyth)
  • Ontology Mapping for the Laboratory Analytics Domain (Ian Harrow, Thomas Liener and Ernesto Jimenez-Ruiz)
  • OME Core Ontology: An OWL-based Life Science Imaging Data Model (Norio Kobayashi, Josh Moore, Shuichi Onami and Jason R. Sewdlow)
  • The 4DN-OME ontology: an OME-OWL extension with emphasis on usability, minimum information guidelines and quality control for super-resolution fluorescence microscopy (Mathias Hammer, Alessandro Rigano, Farzin Farzam, Maximiliaan Huisman, David Grunwald and Caterina Strambio-De-Castillia)
14.50-15.30 Presentations, chaired by Chris Baker:

  • Making clinical trials available at the point of care – connecting Clinical trials to Electronic Health Records using SNOMED CT and HL7 InfoButton standards (Jay Kola, Wai Keong Wong and Bhavana Buddala)
  • A Blueprint for Semantically Lifting Field Trial Data: Enabling Exploration using Knowledge Graphs (Daniel Burkow, Jens Hollunder, Julian Heinrich, Fuad Abdallah, Miguel Rojas-Macias, Cord Wiljes, Philipp Cimiano and Philipp Senger)
15.30-16.30 Poster and demo session, Coffee break
16.30-18.00 Panel discussion (Spotlight on Agrisemantics II), introduced by Suchith Anand, chaired by Brett Drury

Conference Dinner

Our social event will be a conference dinner taking place at Howies Restaurant in Waterloo Place, just next to Calton Hill.

December 11th – Conference Day 2 – The CAIRN Auditorium

8.30-9.00 Registration
9.00-9.15 Recap from the previous day, by Ronald Cornet
9.15-10.00 Keynote by Dov Greenbaum, introduced by Ronald Cornet
Data Ownership and protection within the FAIR Framework
10.00-10.40 Presentations, chaired by Ronald Cornet:

  • Documentation Gap in Ontology Creation: Insights into the Reality of Knowledge Formalization in a Life Science Company (Marius Michaelis and Olga Streibel)
  • Partitioning of BioPortal Ontologies: An Empirical Study (Alsayed Algergawy and Birgitta König-Ries)
10.40-11.10 Coffee break
 11.10-12.30 Presentations, chaired by Andrea Splendiani:

  • Annotation of existing databases using Semantic Web technologies: making data more FAIR (Johan van Soest, Ananya Choudhury, Nikhil Gaikwad, Matthijs Sloep, Michel Dumontier and Andre Dekker)
  • FAIRness of openEHR Archetypes and Templates (Caroline Bönisch, Anneka Sargeant, Antje Wulff, Marcel Parciak, Christian R Bauer and Ulrich Sax)
  • A Working Model for Data Integration of Occupation, Function and Health (Anil Adisesh, Mohammad Sadnan Al Manir, Hongchang Bao and Christopher Baker)
  • FAIR quantitative imaging in oncology: how Semantic Web and Ontologies will support reproducible science (Alberto Traverso, Zhenwei Shi, Leonard Wee and Andre Dekker)
12.30-13.30 Lunch break
13.30-14.15 Keynote by Helen Parkinson, introduced by Chris Baker
A FAIR Vocabulary Odyssey
14.15-14.45 Lightning poster & demo presentations, chaired by Andra Waagmeester:

  • Babylon Health’s Medical Knowledge Graph: Why, What, and How (Claudia Schulz, Damir Juric, Jetendr Shamdasani, Martin Coste, Szymon Wartak, Aleksandar Savkov, Nils Hammerla and Mohammad Khodadadi)
  • Transformation and integration of heterogeneous health data in a privacy-preserving distributed learning infrastructure (Chang Sun, Vincent Emonet, Johan van Soest, Annemarie Koster, Andre Dekker and Michel Dumontier)
  • Semantic Integration of Intrinsically Disordered Proteins and Existing DBs (Atsuko Yamaguchi, Hideki Hatanaka, Satoshi Fukuchi and Motonori Ota)
  • Umaka data extension: Towards Realisation of Practical SPARQL Endpoint Discovery Service for Life Sciences (Norio Kobayashi, Yasunori Yamamoto and Atsuko Yamaguchi)
  • Finding the best RDF data by Umaka Suite (Yasunori Yamamoto and Atsuko Yamaguchi)
  • Species Association Knowledge Graph Construction – A Demo Paper (Dina Sharafeldeen, Alsayed Algergawy and Birgitta König-Ries)
  • Med2RDF: Semantic Biomedical Knowledge-base and APIs for the Clinical Genome Medicine (Mayumi Kamada, Toshiaki Katayama, Shuichi Kawashima, Ryosuke Kojima, Masahiko Nakatsui and Yasushi Okuno)
  • MetaStanza: Generic WebComponents Widgets for Visualizing SPARQL Results on the Web (Toshiaki Katayama)
  • Integrated Growth Media Database by Standardizing Ingredient Information (Shuichi Kawashima, Toshiaki Katayama, Yuki Moriya, Shinobu Okamoto, Yasunori Yamamoto and Susumu Goto)
  • SemanticGenomeGraphs (Simon Heumos and Jerven Bolleman)
  • Network building with Cytoscape App queries to the BioGateway 3.0 triple store (Stian Holmås, Vladimir Mironov and Martin Kuiper)
  • Semantic models for pharma: Connecting data across drug discovery (Ilaria Maresi, Jochem Bijlard and Kees Van Bochove)
14.45-15.45 Poster and demo session, Coffee break
15.45-16.45 Panel discussion, chaired by Scott Marshall
16.45-17.00 Conference wrap-up & Hackathon outlook, by Albert Burger, Ronald Cornet & Andra Waagmeester

December 12th – Hackathon – The GRID

Room: Inspire and Collaborate 2 (Ground Floor)

8.30-9.00 Coffee
9.00-9.15 Welcome, Introduction and Pitches
9.15-12.00 Hack, explore, discuss, mingle.
12.00 interim results
12.00-14.30 Hack, explore, discuss, mingle.
14.30-15.30 Results and Demonstrations
15.30-> Hack, explore, discuss, mingle.


All Keynotes, Tutorials, Accepted Papers, Posters and demos are now online.