Semantic Web Applications and Tools for Healthcare and Life Sciences
11th International SWAT4HCLS Conference, Antwerp 2018

Programme

 — Preliminary –

December 3rd Tutorial day

Data and Standards (data and standards: challenges where semantics can make an impact) 

Data science (fundamentals)

Semantics  (Semantic tools and applications)

Room A Room B Room C
9:00-10.30

Data and Standards

Semantic Web in the Pharmaceutical Industry: A Landscape of Challenges and Opportunities

Data Science

Knowledge Discovery and Machine Learning in KNIME (An introduction to Pattern Mining, Clustering and Classification)

Semantics

LOD4CG & BioFed: Publishing and Accessing Large-Scale Cancer and Biomedical Linked Data Resources

Coffee Break
11:00-12.30

Data and Standards

The OMOP common Data Model for observational studies

Data Science

tutorial continues

Semantics

tutorial continues

Lunch Break
13.30-15.00

Data and Standards

HL7 FHIR and the Semantic Web

Data and Standards

Agricultural semantics: challenges, opportunities and the AgroFIMS fieldbook

Semantics

Bioschemas: a lightweight semantic layer for Life Sciences

Coffee Break
15.30-17.00

Semantics

Wikibase

Data and Standards

tutorial continues

Semantics

The CEDAR Workbench: Enhanced Authoring of Standards-Based Metadata for use on the Semantic Web

Reserved (17-18)

Data and Standards

openEHR

    Reception

December 4th-5th Conference days

Conference day 1

8.30-9.00 Registration
9.00-9.15 Welcome, introduction. Outline of the conference and hackathon
9.15-10.00

Keynote by Philip Bourne

How Does Data Science Impact the Semantic Web?

10.00-10.35

Selected Talks

Using semantic technologies to enhance metadata submissions to public repositories in biomedicine. Attila L. Egyedi, Martin O’Connor, Marcos Martínez-Romero, Debra Willrett, Josef Hardi, John Graybeal and Mark Musen.

Using Wikidata for semantic data modeling in education and research. Annika Jacobsen, Andra Waagmeester, Rajaram Kaliyaperumal, Greg Stupp, Lynn Schriml, Mark Thompson, Andrew I. Su and Marco Roos.  (short paper)

10.35-11.15 Coffee break
11.15-12.30

Selected talks

The Story of an Experiment: A Provenance-based Semantic Approach towards Research Reproducibility. Sheeba Samuel, Kathrin Groeneveld, Frank Taubert, Daniel Walther, Tom Kache, Teresa Langenstück, Birgitta König-Ries, Martin Buecker and Christoph Biskup. 

DSAP: Data Sharing Agreement Privacy Ontology. Mingyuan Li and Reza Samavi. 

A model for capturing provenance of assertions about chemical substances. Kody Moodley, Amrapali Zaveri, Chunlei Wu and Michel Dumontier. 

Increasing the nanopublication recall with a BridgeDb Identifier Mapping Service. Egon Willighagen. (short paper) 

12.30-13.30 Lunch break
13.30-14.15

Keynote by Medha Devare

Spinning a Semantic Web for Agriculture

14.15-15.10

Selected talks

Design of a framework to support reuse of Open Data about agriculture. Alec Gordon, Mohammad Sadnan Al Manir, Brandon Smith, Amir Hossein Rezaie and Christopher Baker. 
TBD (Short Talk)
Ontology-Driven Metadata Enrichment for Genomic Datasets. Anna Bernasconi, Arif Canakoglu, Andrea Colombo and Stefano Ceri. 

15.10-15.30 Lightning poster presentations
15.30-16.30 Poster and demo session, Coffee break
16.30-18.00

Panel discussion (Agrisemantics)

André LaperrièreChristopher BrewsterThomas BakerGraham Mullier and Matthew Lange

Social dinner

Conference day 2

8.30-9.00 Registration
9.00-9.15 Recap from the previous day
9.15-10.00 TBD
10.00-10.40

Selected Talks

Sparklis over PEGASE Knowledge Graph: A New Tool for Pharmacovigilance. Carlos Bobed, Laura Douze, Sébastien Ferré and Romaric Marcilly. 

Allotrope Data Format – Semantic Data Management in Life Sciences. Heiner Oberkampf, Helge Krieg, Christian Senger, Thomas Weber and Wolfgang Colsman. (Industry report)

Architecture for the harmonization of clinical cohort data in the IMI EMIF project. Rudi Verbeeck, Luiza Gabriel and Michel van Speybroeck. (Industry report)

10.40-11.15 Coffee break
11.15-12.30

Selected talks

A Distributed Analytics Platform to Execute FHIR based Phenotyping Algorithms. Md. Rezaul Karim, Binh-Phi Nguyen, Lukas Zimmermann, Toralf Kirsten, Matthias Löbe, Frank Meineke, Holger Stenzhorn, Oliver Kohlbacher, Stefan Decker and Oya Beyan. 

A Semantic Data Integration Methodology for Translational Neurodegenerative Disease Research. Sumit Madan, Maksims Fiosins, Stefan Bonn and Juliane Fluck. 

Cooperation of bio-ontologies for the classification of genetic intellectual disabilities : a diseasome approach. Gabin Personeni, Marie-Dominique Devignes, Malika Smail-Tabbone, Philippe Jonveaux, Céline Bonnet and Adrien Coulet.

Progress Towards an Ontology Mapping Service. Industry (38) Ian Harrow, Martin Romacker, Andrea Splendiani, Peter Woollard, Tom Plasterer, Rainer Winnenburg, Scott Markel, Siddharth Mehta, Chris Piddington, Yasmin Alam-Faruque, Rama Balakrishnan, Jane Lomax, Jane Reed, Christian Senger, Jabe Wilson, Filip Pattyn, Ernesto Jimenez-Ruiz and Simon Jupp.  (Industry report)

12.30-13.30 Lunch break
13.30-14.15

Keynote by Dean Allemang

Semantic Web and the New Industrial Revolution

14.15-14.55

Selected talks

Evaluation of Knowledge Graph Embedding Approaches for Drug-Drug Interaction Prediction using Linked Open Data. Remzi Çelebi, Erkan Yaşar, Hüseyin Uyar, Özgür Gümüş, Oguz Dikenelli and Michel Dumontier.  

Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings. Maxat Kulmanov, Senay Kafkas, Andreas Karwath, Alexander Malic, Georgios V Gkoutos, Michel Dumontier and Robert Hoehndorf.  

14.55-16.00 Poster and demo session, Coffee break
16.00-16.40

Selected talks

Data2Services: enabling automated conversion of data to services. Vincent Emonet, Amrapali Zaveri, Alexander Malic, Andreea Grigoriu and Michel Dumontier. 
Getting the best of Linked Data and Property Graphs: rdf2neo and the KnetMiner Use Case. Marco Brandizi, Ajit Singh and Keywan Hassani-Pak.

16.40-17.30 Healthcare interoperability panel (provisional)

December 6th Hackathon day

Feel free to add your idea to the hackathon brainstorming doc!