July, 16th (Wednesday) – together with the Data Storm Big Data Summer School
6:30 PM: Open DILS registration (Salão Nobre)
6:45 PM – 7:30 PM: Visit to the Alfredo Bensaúde Museum (IST)
7:30 PM – 9:00 PM: Welcome Reception (IST Garden near the Kindergartner)
July, 17th (Thursday) – Salão Nobre
8:30 AM: Registration
9:00 AM – 10:30 AM: Welcome and keynote session (Session chair: Helena Galhardas)
Computational Biology and Big Data: Challenges and Opportunities
Alfonso Valencia
10:30 AM – 11:00 AM: Coffee Break
11:00 AM – 12:45 PM: Paper session: Data Integration Platforms and Applications
(Session chair: Erhard Rahm)
An Asset Management Approach to Continuous Integration of Heterogeneous Biomedical Data
Robert Schuler, Carl Kesselman and Karl Czajkowski
(Univ. of Southern California, USA)
Mining Linked Open Data: a Case Study with Genes Responsible for Intellectual Disability (Application paper)
Gabin Personeni, Simon Daget, Céline Bonnet, Philippe Jonveaux, Marie-Dominique Devignes, Malika Smaïl-Tabbone and Adrien Coulet
(LORIA, Univ. of Nancy and Univ. of Lorraine, France)
Data integration between Swedish national clinical health registries and biobanks using an availability system (Application paper)
Ola Spjuth, Jani Heikkinen, Jan-Eric Litton, Juni Palmgren and Maria Krestyaninova
(Karolisnka Institute Stockholm, Sweden and Univ. of Helsinki, Finland)
Advertisement of posters and demos
- Bioinformatics for Operational Precision Medicine in Oncology: application to the SHIVA clinical trial Philippe Hupé (Institut Curie, France)
- The GigaSolution to data publication, reuse and integration (demo) Christopher Hunter, Peter Li, Xiao Si Zhe, Robert Davidson, Laurie Goodman and Scott C. Edmunds (GigaScience, Hong Kong)
- The MicroScope platform: from data integration to a rule-based system for massive and high-quality microbial genome annotation Jonathan Mercier, Alexandre Renaux, Adrien Josso, Aurélie Genin-Lajus, E’Krame Jacoby, François Le Fevre, Guillaume Albini, Claude Scarpelli, Claudine Medigue and David Vallenet (CEA Genoscope, France)
- The e!DAL Java API: Sharing and Citing Research Data in Life Sciences Daniel Arend, Jinbo Chen, Christian Colmsee, Steffen Flemming, Denny Hecht, Uwe Scholz and Matthias Lange (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Germany)
- Identifiers.org: integration tool for heterogeneous datasets (demo) Camille Laibe, Sarala Wimalaratne, Nick Juty, Nicolas Le Novère and Henning Hermjakob (EMBL-EBI and Babraham Institute, UK)
- Search QTL candidate genes by LAILAPS information retrieval system Jinbo Chen, Daniel Arend, Christian Colmsee, Maria Esch, Uwe Scholz and Matthias Lange (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Germany)
- PRIDE Proteomes: a condensed view of the plethora of public proteomics data available in the PRIDE repository Noemi Del Toro Ayllón, Florian Reisinger, Antonio Fabregat Mundo, Pau Ruiz Safont, Henning Hermjakob and Juan A Vizcaíno (EMBL-EBI, UK)
12:45 PM – 2:00 PM: Lunch Break (Lunch Bags)
2:00 PM – 3:45 PM: Paper session: Biodiversity Data Management
(Session chair: Francisco Couto)
Data management experiences and best practices from the perspective of a plant research institute (Application paper)
Daniel Arend, Christian Colmsee, Helmut Knüpffer, Markus Oppermann, Uwe Scholz, Danuta Schüler, Stephan Weise and Matthias Lange
(IPK Gatersleben, Germany)
A semantic web faceted search system for facilitating building of biodiversity and ecosystems services
Marie-Angélique Laporte, Isabelle Mougenot, Eric Garnier, Ulrike Stahl, Jens Kattge and Lutz Maicher
(iDiv Halle-Jena-Leipzig and Max-Planck-Institute Jena, Germany, and UMR Montpellier, France)
Handling Multiple Foci in Graph Databases
Jaudete Daltio and Claudia Bauzer Medeiros
(Univ. of Campinas, Brazil)
Advertisement of posters and demos
- A Machine Learning based Natural Language Interface for a database of medicines Ricardo Ferrão, Helena Galhardas and Luísa Coheur (Instituto Superior Técnico, Univ. of Lisbon and INESC-ID, Portugal)
- AgreementMakerLight: A Scalable Automated Ontology Matching System (demo) Daniel Faria, Catia Pesquita, Emanuel Santos, Isabel F. Cruz and Francisco Couto (Faculdade de Ciências, Univ. of Lisbon, Portugal, and University of Illinois, USA)
- Towards a Linked Biology – An integrated perspective of phenotypes and phylogenetic trees Eduardo Miranda, Anaïs Grand, Régine Vignes Lebbe and André Santanchè (Universidade de Campinas, Brazil, Muséum National d’Histoire Naturelle de Paris and UPMC Univ Paris 06, France)
- Developments and perspectives for CABRI Web Services Daniele Pierpaolo Colobraro and Paolo Romano (IRCCS University Hospital San Martino IST, Italy)
- Towards a Plant Experimental Assay Ontology Nuno D. Mendes, Pedro T. Monteiro, Cátia Vaz and Inês Chaves (INESC-ID, iBET, ISEL and ITQB, Portugal)
- Identifying, interpreting, and communicating changes in XML-encoded models of biological systems Martin Scharm, Olaf Wolkenhauer and Dagmar Waltemath (Universität Rostock, Germany)
- REX – a tool for discovering evolution trends in ontology regions(demo) Victor Christen, Anika Groß and Michael Hartung (Universität Leipzig, Germany)
- A Repository for Biological Data applied to the Woody Plants Domain Filipa Rebelo, Inês Chaves, Nuno D. Mendes, Pedro T. Monteiro and José Borbinha (INESC-ID, iBET, ISEL, ITQB and Instituto Superior Técnico, Univ. of Lisbon, Portugal)
3:45 PM – 4:15 PM: Coffee Break
4:15 PM – 6:00 PM: Posters and Demos
8:00 PM: Banquet (Via Graça Restaurant)
July, 18th (Friday) – Salão Nobre
9:00 AM – 10:00 AM: Keynote session (Chair: Erhard Rahm)
The emergence of the Web Computer: an hands-on view from the trenches of Computational Pathology
Jonas Almeida
10:00 AM – 10:30 AM: Coffee Break
10:30 AM – 12:30 AM: Paper session: Ontologies and Visualization
(Session chair: Maria-Esther Vidal)
Completing the is-a structure of biomedical ontologies
Zlatan Dragisic, Patrick Lambrix and Fang Wei-Kleiner
(Linköping University, Sweden)
Annotation-based feature extraction from sets of SBML models
Rebekka Alm, Dagmar Waltemath, Olaf Wolkenhauer and Ron Henkel
(Fraunhofer Institute and Univ. of Rostock, Germany)
REX – a tool for discovering evolution trends in ontology regions (System paper)
Victor Christen, Anika Groß and Michael Hartung
(Univ. of Leipzig, Germany)
Towards visualizing the alignment of large biomedical ontologies (System paper)
Catia Pesquita, Daniel Faria, Emanuel Santos and Francisco Couto
(Univ. of Lisbon, Portugal)
12:30 PM – 2:00 PM: Lunch Break (Lunch Bags)
2:00 PM – 4:00 PM: Paper session: Linked Data and Query Processing
(Session chair: Dagmar Waltemath)
Discovering Relations between Indirectly Connected Biomedical Concepts
Dirk Weissenborn, Michael Schroeder and George Tsatsaronis
(TU Dresden, Germany)
Exploiting Semantics from Ontologies and Shared Annotations to Partition Linked Data
Guillermo Palma, Maria-Esther Vidal, Louiqa Raschid and Andreas Thor
(Univ. Simon Bolivar, Venezuela, Univ. of Maryland, USA, and Univ. of Leipzig, Germany)
ConQuR: Consensus ranking with Query Reformulation on biological data
Bryan Brancotte, Bastien Rance, Alain Denise and Sarah Cohen-Boulakia
(Univ. Paris-Sud and Univ.Hospital HEGP Paris, France)
An Introduction to the Data Retrieval Facilities of the XQt Language for Scientific Data
Javad Chamanara and Birgitta König-Ries
(FSU Jena, Germany)
4:00 PM – 4:15 PM: Concluding Remarks
(Session chair: Helena Galhardas)
4:15 PM – 4:45 PM: Coffee Break
