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. |
