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Main Conference 6th – 7th December

Tentative programme

Location:

Piet Borst Auditorium (PBA), Netherlands Cancer Institute in Amsterdam

Jump to:
Tutorials
Conference day one
Conference day two
Accepted poster
Hackathon

Tentative programme day one, 6th December
Time Title Type Chair
08:30 Registration & coffee/tea – Foyer
09:00 Welcome
09:10 Drug Discovery and Big Linked Data – Ronald Siebes, Victor de Boer, Bryn Williams-Jones and Stian Soiland-Reyes. Flash
09:15 Umaka-Yummy Data: A Place to Facilitate Communication between Data Providers and Consumers – Yasunori Yamamoto, Atsuko Yamaguchi and Andrea Splendiani. Flash
09:20 Semantic Web technologies for a knowledge base of biomedical facts extracted from scientific literature – Valentin Grouès, Maria Biryukov, Christophe Trefois and Venkata Satagopam. Flash
09:25 Linking Wikidata to the rest of the Semantic Web – Andra Waagmeester, Egon Willighagen, Núria Queralt Rosinach, Elvira Mitraka, Sebastian Burgstaller-Muehlbacher, Tim E Putman, Julia Turner, Lynn M Schriml, Paul Pavlidis, Andrew I Su and Benjamin M Good. Flash
09:30 Scaling out ETL queries for Life Science data in productionDieter De Witte, Laurens De Vocht, Kenny Knecht, Filip Pattyn, Hans Constandt, Erik Mannens and Ruben Verborgh.  Long
09:50 Ontologies Guidelines and Evaluation of Ontologies Mapping Tools and Algorithms – Ian Harrow, Martin Romacker, Andrea Splendiani, Stefan Negru, Peter Woollard, Scott Markel, Yasmin Alam-Faruque, Martin Koch, Erfan Younesi, James Malone and Ernesto Jimenez-Ruiz. Flash
09:55 Finding drugs with common downstream effects, using direction information in biological pathways – Ryan Miller, Jonathan Melius, Nuno Nunes, Egon Willighagen, Peter Woollard and Chris Evelo. Flash
10:00 SPARQL Query Construction with Monitoring Service for Endpoints – Atsuko Yamaguchi, Yasunori Yamamoto, Kouji Kozaki, Kai Lenz, Hiroshi Masuya and Norio Kobayashi. Flash
10:05

Updates from the EMBL-EBI RDF platform – Thomas Liener, Tony Burdett and Simon Jupp.

Flash
10:10 FLOPO An Ontology for the Integration of Trait Data from Digitized Floras and Plant Image Collections – Claus Weiland, Robert Hoehndorf, George Gosline, Quentin Groom, Thomas Hamann and Marco Schmidt. Flash
10:15 HL7 FHIR and Schema.org – Harold Solbrig, Eric Prud’Hommeaux and Guoqian Jiang. Flash
10:20 Answering scientific questions with linked European nanosafety data – Egon Willighagen, Micha Rautenberg, Georgios Drakakis, Haralambos Sarimveis, Christoph Helma and Nina Jeliazkova. Flash
10:25 Ontology-based reflective Iot middleware-enabled agriculture decision support system – Tommaso Di Noia, Marina Mongiello, Francesco Nocera and Eugenio Di Sciascio Flash
10:30 Break – Foyer
11:00 Registries of domain-relevant semantic reference models help bootstrap interoperability in domains with fragmented data resources – Marco Roos, Mark Wilkinson, Rajaram Kaliyaperumal, Mark Thompson, Claudio Carta, Ronald Cornet, David van Enckevort and Luiz Olavo Bonino Da Silva Santos.  Long
11:20 The organisation of Bring Your Own Data (BYOD) workshops to make life science data linkable at the source – Mascha Jansen, Claudio Carta, Marco Roos and Luiz Olavo Bonino Da Silva Santos. Flash
11:25 Semantic linking and integration of researchers and research organizations in DISQOVER – Filip Pattyn, Steven Vandeschaeve, Stijn Vermaere, Paulo Van Huffel, Kenny Knecht and Hans Constandt. Flash
11:30 A poster about a new graph-based taxonomy RESTful data service – Leyla Jael García Castro, Leonardo Gonzales and Maria Martin. Flash
11:35 AgroLD indexing tools with ontological annotations – Stella Zevio, Nordine El Hassouni, Manuel Ruiz and Pierre Larmande. Flash
11:40 Semantic and Interoperability in a Reporting System for Infectious Disease Control - Olga Streibel and Göran Kirchner. Flash
11:45 Lunch & poster presentations – Foyer
13:30 Keynote lecture by Amos BairochTransitioning from textual to semantic biocuration, current efforts and perspectives  Key
14:20 Progressive Data Integration and Semantic Enrichment Based on LinkedScales and Trails – Matheus Silva Mota, Fagner Pantoja, Julio Cesar Dos Reis and André Santanchè.  Long
14:40 MuEVo, a breast cancer Consumer Health Vocabulary built out of web forums – Solène Eholié, Mike Donald Tapi Nzali, Sandra Bringay and Clement Jonquet.  Long
15:00 Break – Foyer
15:30 Studying the Cohesion Evolution of Genes Related to Chronic Lymphocytic Leukemia Using Semantic Similarity in Gene Ontology and Self-Organizing Maps – Efstratios Kontopoulos, Theodoros Moysiadis, Maria Tsagiopoulou, Sándor Darányi, Peter Wittek, Nikos Papakonstantinou, Stavroula Ntoufa, Georgios Meditskos, Yiannis Kompatsiaris and Kostas Stamatopoulos  Long
15:50 SCRY: extending SPARQL with custom data processing methods for the life sciences – Bas Stringer, Albert Meroño-Peñuela, Sanne Abeln, Frank Van Harmelen and Jaap Heringa.  Long
16:10 Slim-o-matic: a semi-automated way to generate Gene Ontology slims – Melanie Courtot, Alex Mitchell, Maxim Scheremetjew, Janet Piñero, Laura I. Furlong, Robert D. Finn and Helen Parkinson. Short
16:20 Keynote lecture by Martin Hofmann-ApitiusBioMedical Semantics at Work: The AETIONOMY Project  Key
17:10 Close
 17:15 Bus to boat embarcation
18:00 Boat past Amsterdam Light Festival to restaurant. Read more.
19:30 Conference dinner
citylights1
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Tentative programme day two, 7th December

Time Title Type Chair
08:45 Registration & coffee/tea – Foyer
09:15 Welcome
09:25 Making Linked Data SPARQL with the InterMine Biological Data Warehouse – Maxime Déraspe, Gail Binkley, Daniela Butano, Matthew Chadwick, J. Michael Cherry, Justin Clark-Casey, Sergio Contrino, Jacques Corbeil, Josh Heimbach, Kalpana Karra, Rachel Lyne, Julie Sullivan, Yo Yehudi, Gos Micklem and Michel Dumontier  Long
09:45 Ontology Learning with Deep Learning: a case study on Patient Safety using PubMed – Mercedes Arguello Casteleiro, Maria Jesus Fernandez-Prieto, George Demetriou, Nava Maroto, Warren Read, Diego Maseda Fernandez, Jose Julio Des Diz, Goran Nenadic, John Keane and Robert Stevens.  Long
10:05 A RDF Based Semantic Approach to Model Temporal Relations in Health Records – Oya Beyan and Stefan Decker.  Short
10:15 Towards the Creation of the Cardiovascular Magnetic Resonance Quality Assessment Ontology (CMR-QA) – Ernesto Jimenez-Ruiz, Valentina Carapella, Elena Lukaschuk, Nay Aung, Kenneth Fung, Jose Paiva, Mihir Sanghvi, Stefan Neubauer, Steffen Petersen, Ian Horrocks and Stefan Piechnik.  Short
10:25 WHO Drug as Linked Data – Magnus Wallberg  Flash
10:30 Break – Foyer
11:00 Case Report Form based on semantic Web technologies – Angel Esteban-Gil and Jesualdo Tomás Fernández-Breis.  Long
11:20 Discovering Information from an Integrated Graph Database – Erik van Mulligen, Wytze Vlietstra, Rein Vos and Jan Kors.  Long
11:40 SWISH for prototyping Clinical Guideline Interactions Theory – Veruska Zamborlini, Jan Wielemaker, Marcos Da Silveira, Cédric Pruski, Annette Ten Teije and Frank Van Harmelen.  Long
12:00 Lunch & poster presentations – Foyer
13:30 Keynote lecture by Dietrich Rebholz-SchuhmannSemantics driven big data analytics: Ongoing work for cancer genomics  Key
14:20 Understanding the Behaviour of Complex Biomolecular Networks by Combining Logical and Semantic Modeling – Ali Ayadi, Cecilia Zanni-Merk and Franc ̧ois de Bertrand de Beuvron.  Long
14:40 Web Service APIs for Scribe Registrars, Nexus Diristries, PORTAL Registries and DOORS Directories in the NPD System – Adam Craig, Seung-Ho Bae, Teja Veeramacheneni, Koby Taswell and Carl Taswell.  Short
14:50 Easy-to-use semantic search of pharmacological data – Guillermo Vega-Gorgojo and Laura Slaughter Short
15:00 Break – Foyer
15:30 Semantic PACS – Concept, Benefit and Implementation illustrated by SeDI – Peter Feltens, SOHARD Software GmbH Industry
15:50 Semantic DICOM clinical applications – ​Tomas Janssen Industry
16:10 Ontology-Driven Context Interpretation and Conflict Resolution in Dialogue-Based Home Care Assistance – Georgios Meditskos, Efstratios Kontopoulos, Stefanos Vrochidis and Yiannis Kompatsiaris.  Short
16:20 Capturing the relationship between evolving biomedical concepts via background knowledge  – Cédric Pruski, Julio Cesar Dos Reis and Marcos Da Silveira.  Long
16:40 Semantic Web in Industry Panel
17:00 Close
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Accepted Posters

  1. Updates from the EMBL-EBI RDF platform - Thomas Liener, Tony Burdett and Simon Jupp.
  2. FLOPO An Ontology for the Integration of Trait Data from Digitized Floras and Plant Image Collections – Claus Weiland, Robert Hoehndorf, George Gosline, Quentin Groom, Thomas Hamann and Marco Schmidt.
  3. HL7 FHIR and Schema.org – Harold Solbrig, Eric Prud’Hommeaux and Guoqian Jiang.
  4. Answering scientific questions with linked European nanosafety data – Egon Willighagen, Micha Rautenberg, Georgios Drakakis, Haralambos Sarimveis, Christoph Helma and Nina Jeliazkova.
  5. A poster about a new graph-based taxonomy RESTful data service – Leyla Jael García Castro, Leonardo Gonzales and Maria Martin.
  6. AgroLD indexing tools with ontological annotations – Stella Zevio, Nordine El Hassouni, Manuel Ruiz and Pierre Larmande.
  7. Ontologies Guidelines and Evaluation of Ontologies Mapping Tools and Algorithms – Ian Harrow, Martin Romacker, Andrea Splendiani, Stefan Negru, Peter Woollard, Scott Markel, Yasmin Alam-Faruque, Martin Koch, Erfan Younesi, James Malone and Ernesto Jimenez-Ruiz.
  8. Finding drugs with common downstream effects, using direction information in biological pathways – Ryan Miller, Jonathan Melius, Nuno Nunes, Egon Willighagen, Peter Woollard and Chris Evelo.
  9. SPARQL Query Construction with Monitoring Service for Endpoints – Atsuko Yamaguchi, Yasunori Yamamoto, Kouji Kozaki, Kai Lenz, Hiroshi Masuya and Norio Kobayashi.
  10. The organisation of Bring Your Own Data (BYOD) workshops to make life science data linkable at the source – Mascha Jansen, Claudio Carta, Marco Roos and Luiz Olavo Bonino Da Silva Santos.
  11. Semantic linking and integration of researchers and research organizations in DISQOVER – Filip Pattyn, Steven Vandeschaeve, Stijn Vermaere, Paulo Van Huffel, Kenny Knecht and Hans Constandt.
  12. Drug Discovery and Big Linked Data – Ronald Siebes, Victor de Boer, Bryn Williams-Jones and Stian Soiland-Reyes.
  13. Semantic Web technologies for a knowledge base of biomedical facts extracted from scientific literature – Valentin Grouès, Maria Biryukov, Christophe Trefois and Venkata Satagopam.
  14. Linking Wikidata to the rest of the Semantic Web – Andra Waagmeester, Egon Willighagen, Núria Queralt Rosinach, Elvira Mitraka, Sebastian Burgstaller-Muehlbacher, Tim E Putman, Julia Turner, Lynn M Schriml, Paul Pavlidis, Andrew I Su and Benjamin M Good.
  15. Umaka-Yummy Data: A Place to Facilitate Communication between Data Providers and Consumers – Yasunori Yamamoto, Atsuko Yamaguchi and Andrea Splendiani.
  16. Ontology-based reflective Iot middleware-enabled agriculture decision support system – Tommaso Di Noia, Marina Mongiello, Francesco Nocera and Eugenio Di Sciascio.
  17. Semantic and Interoperability in a Reporting System for Infectious Disease Control – Olga Streibel and Göran Kirchner.