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Main Conference 8th – 9th December

Main Conference Programme
Location: Riley Auditorium, Gillespie Center, Clare College

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Conference day one
Conference day two
Accepted posters – Session A
Accepted posters – Session B


Conference Day One – Tuesday 8th December

Time Title Type Chair
08:30 Registration open – Garden Room
09:00 Welcome – Robert Stevens


Finding novel associations across domains using linked data: a case study on genetic variants disrupting transcription start sites – Eelke van der Horst, Rajaram Kaliyaperumal, Zuotian Tatum, Mark Thompson, Erik Schultes, Eleni Mina, Ivo Fokkema, Johan den Dunnen, Marco Roos, Jeroen Laros, Barend Mons, Kristina Hettne and P.A.C ‘T Hoen Long
Simon Jupp
09:30 iCyrus: A Semantic Framework for Biomedical Image Discovery – Syed Ahmad Chan Bukhari, Mate Nagy, Paolo Ciccarese, Michael Krauthammer and Christopher J.O Baker Long
09:50 Linked Functional Annotation For Differentially Expressed Gene (DEG) Demonstrated using Illumina Body Map 2.0 – Alokkumar Jha, Yasar Khan, Aftab Iqbal, Achille Zappa, Muntazir Mehdi, Ratnesh Sahay and Dietrich Rebholz-Schuhmann Long
10:10 Towards Shared Hypothesis Testing in the Biomedical Domain – Asan Agibetov, Ernesto Jimenez Ruiz, Alessandro Solimando, Giovanna Guerrini, Giuseppe Patanè and Michela Spagnuolo Short
10:20 Glycan pattern search – Davide Alocci, Julien Mariethoz and Frédérique Lisacek Demo
10:30  Break – refreshments in Garden Room
11:00 VacSeen: – A Linked Data-Based Information Architecture to Track Vaccines Using Barcode Scan Authentication – Partha Bhattacharjee, Monika Solanki, Rahul Bhattacharyya, Isaac Ehrenberg and Sanjay Sarma Long
Mélanie Courtot
11:20 Suggesting valid pharmacogenes by mining linked data – Kévin Dalleau, Ndeye Coumba Ndiaye and Adrien Coulet Long
11:40 Flash poster presentations – Session A Flash
Mélanie Courtot & James Malone
12:00 Lunch – Garden Room followed by Poster Session A in Elton-Bowring Room
13:30 Keynote: Representing All Clinical Knowledge – Bijan Parsia Key
Robert Stevens
 14:20 ODM on FHIR: Towards Achieving Semantic Interoperability of Clinical Study Data – Hugo Leroux, Alejandro Metke and Michael John Lawley Long
Chris Baker
 14:40 Wikidata: A platform for data integration and dissemination for the life sciences and beyond – Elvira Mitraka, Andra Waagmeester, Sebastian Burgstaller-Muehlbacher, Lynn M. Schriml, Andrew I. Su and Benjamin M. Good  Short
 14:50 Towards the semantic standardization of orthology content – Jesualdo Tomás Fernández-Breis, María Del Carmen Legaz-García, Hirokazu Chiba and Ikuo Uchiyama Short
15:00  Break – refreshments in Garden Room
15:30 Cell, chemical and anatomical views of the Gene Ontology: mapping to a Roche controlled vocabulary – David Osumi-Sutherland, Enrico Ponta, Melanie Courtot, Helen Parkinson and Laura Badi Long
Robert Hoehndorf
15:50 A Highly Literate Approach to Ontology Building – Phillip Lord and Jennifer Warrender Long
16:10 OBOPedia: An encyclopaedia of biology using OBO ontologies – Robert Stevens and Adam Nogradi Short
16:20 A new Ontology Lookup Service at EMBL-EBI – Simon Jupp, Tony Burdett, Catherine Leroy and Helen Parkinson Demo
16:30 Collaborative Ontology Development Using the Webulous Architecture and Google App – Simon Jupp, Danielle Welter, Tony Burdett, Helen Parkinson, James Malone Demo
16:40 KnowSense: A Semantically-enabled Pervasive Framework to Assist Clinical Autonomy Assessment – Georgios Meditskos, Thanos Stavropoulos and Yiannis Kompatsiaris Short
16:50 Using Semantics and NLP in Experimental Protocols – Olga Giraldo, Alexander Garcia, Oscar Corcho and Jose Figueredo Short
17:00 Close
19:00 Conference Dinner – Garden Room, Clare College
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Conference Day Two – Wednesday 9th December

Time Title Type Chair
09:00 The BioHub Knowledge Base: Ontology and Repository for Sustainable Biosourcing – Warren Read, George Demetriou, Goran Nenadic, Noel Ruddock, Robert Stevens and Jerry Winter Industry
Kerstin Forsberg
09:15 Customizing “General SPARQL” for visualisation of in-house data in Cytoscape – Martijn Van Iersel, Joanna Parmley and Liz Reynolds Industry
09:30 GraphScope – smart data access for the life sciences – Daniel M. Herzig and Günter Ladwig Industry
09:45 Semantic Technologies Make Sense for Life Sciences – Matthieu Jonglez Industry
10:00 Advancing Knowledge Discovery for Alzheimer’s Disease: The Alzforum Experience – Elizabeth Wu Industry
10:15 Everybody a Translational Data Scientist – Hans Constandt Industry
10:30  Break – refreshments in Garden Room
11:00 R2RML-based access and querying to relational clinical data with morph-RDB – Freddy Priyatna, Raul Alonso-Calvo, Sergio Paraiso, Gueton Padron-Sanchez and Oscar Corcho Long
Elvira Mitraka
11:20 D2RQ Mapper – Yasunori Yamamoto and Toshiaki Katayama Demo
11:30 Cochrane PICO Annotator and PICOfinder: Using semantically-enabled evidence to find what works in health care – Chris Mavergames, Lorne Becker, Irfan Dawood, Anthony Hughes and Julian Everett Demo
11:40 Flash poster presentations – Session B Flash
Elvira Mitraka & James Malone
12:00 Lunch – Garden Room followed by Poster Session B in Elton-Bowring Room
13:30 Keynote: “Not everyone can become a great artist; but a great artist can come from anywhere”: Envisioning a world where everyone helps solve disease – Melissa Haendel Key
James Malone
14:20 Validata: An online tool for testing RDF data conformance – Jacob Baungard Hansen, Andrew Beveridge, Roisin Farmer, Leif Gehrmann, Alasdair Gray, Sunil Khutan, Tomas Robertson and Johnny Val Long
Andrea Splendiani
14:40 Exposing Provenance Metadata Using Different RDF Models – Gang Fu, Evan Bolton, Núria Queralt, Laura I. Furlong, Vinh Nguyen, Amit Sheth, Olivier Bodenreider and Michel Dumontier Long
15:00  Break – refreshments in Garden Room

Discussion Panel – Theme: Semantic Web applications and tools in health and life sciences: niche topic or mainstream method? 

Frank Gibson – Royal Society of Chemistry,
Harold Solbrig – Mayo Clinic,
Egon Willighagen – Maastricht University,
Jun Zhao, University of Oxford

Phillip Lord
17:00 Valediction and award ceremony
17:15 Close
Hackathon tomorrow at EBI!
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Note: Poster boards will be 2m high x 1m wide. Velcro will provided for fixing.

Accepted Posters – Session A

  1. Towards Enabling the Semantic Access of Phenotypic Information in Clinical Letters – Shahad Kudama, Rafael Berlanga, Henry Houlden, Ernesto Jimenez-Ruiz, Hallgeir Jonvik, Adam Milward, Huw Morris, Mina Ryten, Jake Saklatvala, Michael Simpson and Nicholas Wood.
  2. OncoCL-KB, a knowledgebase for integration of clinical and molecular cancer data – Mary E Dolan.
  3. COPO – Linked Open Infrastructure for Plant Data – Felix Shaw, Anthony Etuk, Alejandra Gonzalez-Beltran, Phillip Rocca-Serra, Paul Kersey, Ruth Bastow, Susanna-Assunta Sansone, Vicky Schneider and Robert Davey.
  4. Visualising ontologies with AberOWL – Miguel Ángel Rodríguez-García, Luke Slater, Keiron O’Shea, Paul Schofield, Georgios Gkoutos andRobert Hoehndorf.
  5. Towards an Imaging Biomarker Ontology based on the Open Biological and Biomedical Ontologies Foundry – Emna Amdouni, Yannick Morvan and Bernard Gibaud
  6. RDF-Based Integration with SPARQL Building System for Life Science Database Archive – Atsuko Yamaguchi, Katsuhiko Okubo, Norio Kobayashi, Kouji Kozaki, Sadahiro Kumagai, Kai Lenz, Tomoe Nobusada, Hongyan Wu, Yasunori Yamamoto and Hideki Hatanaka
  7. From letters to pixels – Kenneth McLeod, Albert Burger, Christopher Armit, Bill Hill and Richard Baldock.
  8. Performance evaluation of human resources in a hospital – Angel Esteban-Gil, Jesualdo Tomás Fernandez-Breis and Clara Miranda-Lopez.
  9. “Where do you go from here?” Semantics of directions in biological pathways – Ryan Miller, Martina Kutmon, Egon Willighagen, Andra Waagmeester, Jonathan Melius, Anwesha Bohler, Nuno Nunes, Peter Woollard and Chris Evelo.
  10. Digital Dr. House: A semantic alerting platform for the ICU – Femke Ongenae, Bram Gadeyne, Femke De Backere, Liesbet De Bus, Pieter Depuydt, Johan Decruyenaere and Filip De Turck.
  11. Automated Generation of SADI Web Services for Clinical Intelligence using Ruled-Based Semantic Mappings – Mohammad Sadnan Al Manir, Alexandre Riazanov, Harold Boley, Artjom Klein and Christopher J.O. Baker.
  12. GraphScope – the smart data access engine for RDF – Daniel M. Herzig and Günter Ladwig.
  13. Exposing French agronomic resources as Linked Open Data – Aravind Venkatesan, Nordine El Hassouni, Florian Philippe, Cyril Pommier, Hadi Quesneville, Manuel Ruiz and Pierre Larmande.
  14. Feasibility of Modeling HL7 FHIR Profiles Using RDF Shape Expressions Language – Harold Solbrig, Eric Prud’hommeaux, Deepak Sharma, Christopher Chute and Guoqian Jiang.
  15. Semantically indexed resources to facilitate data integration in the Agronomic domain – International Data Discovery System – Florian Philippe, Aravind Venkatesan, Nordine El Hassouni, Cyril Pommier, Manuel Ruiz, Pierre Larmande and Hadi Quesneville.
  16. RDF-based data sharing of bio-resource related information – Hiroshi Masuya, Terue Takatsuki, Mikako Saito, Eiki Takayama, Kazuya Ohshima, Nozomu Ohshiro, Kai Lenz, Nobuhiko Tanaka, Hiroshi Mori, Shuichi Kawashima and Norio Kobayashi.
  17. RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource – Jesse CJ van Dam, Jasper J Koehorst, Peter J Schaap, Vitor AP Martins dos Santos and Maria Suarez-Diez.
  18. NanoText It, a reusable Semantic Web annotation platform for Life Sciences – Alexander Garcia, Oscar Corcho, Federico Lopez, James Anderson and Arto Bendiken.
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Accepted Posters – Session B

  1. Semantic-Web Access to Patent Annotations – Anna Gaulton, Lee Harland, Mark Davies, George Papadatos, Antonis Loizou, Nathan Dedman, Daniela Digles, Stian Soiland-Reyes, Valery Tkachenko, Stefan Senger, John Overington and Nick Lynch.
  2. SCRY: Enabling quantitative reasoning in SPARQL queries – Bas Stringer, Albert Meroño-Peñuela, Antonis Loizou, Sanne Abeln and Jaap Heringa.
  3. Development of the eNanoMapper ontology and usability within the nanosafety domain – Linda Rieswijk, Thies Oosterwijk, Janna Hastings, Friederike Ehrhart, Chris T. Evelo and Egon L. Willighagen.
  4. Insilico precision breeding using interoperable genome annotations and literature – Gurnoor Singh, Arnold Kuzniar, Anand Gavai, Richard Visser and Richard Finkers.
  5. Automatic Synthesis of Bioconductor Pipelines: A Domain Modeling Challenge – Anna-Lena Lamprecht and Tiziana Margaria.
  6. SPANG: a command-line client supporting query generation for distributed SPARQL endpoints – Hirokazu Chiba and Ikuo Uchiyama.
  7. HDT RDF for Biosciences Databases – Alexander Garcia.
  8. Using BioPortal as a Repository for Mediating Ontologies in Ontology Alignment – Weiguo Xia, Ernesto Jimenez-Ruiz and Valerie Cross.
  9. RIKEN Meta Database: a life-science metadata database based on the Semantic Web – Norio Kobayashi, Kai Lenz and Hiroshi Masuya.
  10. Evaluating the Capacity of Open, Linked Data Sources to Assess Adverse Drug Reaction Signals – Vasileios Koutkias, Pantelis Natsiavas and Nicos Maglaveras.
  11. UniProt-GOA: A central resource for data integration and GO annotation  – Melanie Courtot, Aleksandra Shypitsyna, Elena Speretta, Alexander Holmes, Tony Sawford, Tony Wardell, Maria J. Martin and Claire O’Donovan.
  12. Dem@Care: Ambient Sensing and Intelligent Decision Support for the Care of Dementia – Thanos Stavropoulos, Georgios Meditskos and Ioannis Kompatsiaris.
  13. SPARQL Playground – Daniel Teixeira, Alain Gateau, Olivier Evalet, Frederic Nikitin, Jerven Bolleman, Monique Zahn, Pascale Gaudet, Lydie Lane, Amos Bairoch and Pierre-Andre Michel.
  14. Information from Semantic Integration of Texts and Databases – Erik van Mulligen, Wytze Vlietstra, Rein Vos and Jan Kors.
  15. Measuring the Usability of Triple Stores for Knowledge Management on Trauma Care Organizations – Joseph Utecht and Mathias Brochhausen.
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