Public symposium of the BioHackathon 2015 will be held at the Ryojun Kaikan, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki , Japan, on Sep 13 (Sun).
[NEW] Video recordings of the selected symposium talks are made available on YouTube.
Note for speakers: Please try to leave few minutes for Q&A within a given slot.
- 8:30 Meet up at the hotel lobby
- 9:00 Registration opens
- 10:00 Introduction and biomedical semantic resources
10:00-10:10 |
Introduction to the BioHackathon 2015 |
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Toshiaki Katayama Database Center for Life Science, Japan |
10:10-10:25 |
Research at the Atomic Bomb Disease Institute, Nagasaki University |
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Hiroyuki Mishima Nagasaki University, Japan |
10:25-10:40 |
UniProt SPARQL in production |
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Jerven Bolleman Swiss Institute of Bioinformatics, Switzerland |
10:40-10:55 |
PubChemRDF examples, potential applications, and future directions |
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Evan Bolton National Center for Biotechnology Information, USA |
- 10:55 Coffee break
11:10-11:25 |
Efforts in the semantic standardization of orthology content |
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Jesualdo Tomás Fernández-Breis University of Murcia, Spain |
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Applying RDF/SPARQL to ortholog databases |
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Hirokazu Chiba National Institute for Basic Biology, Japan |
11:25-11:40 |
GlycoRDF ontology |
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Thomas Luetteke Justus-Liebig University Giessen, Germany |
11:40-11:55 |
MeSH RDF 2015 |
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Gang Fu National Center for Biotechnology Information, USA |
- 11:55 Group photo
- 12:00 Lunch
- 13:00 Data integration and biomedical applications
13:00-13:15 |
Importance of phenotype data sharing: a proposal from a clinician-researcher on undiagnosed diseases |
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Kenjiro Kosaki Center for Medical Genetics, Keio University School of Medicine, Japan |
13:15-13:30 |
Phenotype Ontologies and their role in understanding rare disorders |
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Tudor Groza Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Australia |
13:30-13:45 |
Introduction of DisGeNET, a discovery platform for the dynamical exploration of human diseases and their genes |
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Núria Queralt Rosinach Institut Hospital del Mar d'Investigacions Mèdiques, Spain |
13:45-14:00 |
Network Analysis and Linking for Bio2RDF |
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Michel Dumontier Stanford University School of Medicine, USA |
14:00-14:15 |
Identifiers.org updates |
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Nick Juty European Bioinformatics Institute, UK |
14:15-14:30 |
YacMa: a semantic web platform for biological knowledge integration |
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Erick Antezana Affiliation: Norwegian University of Science and Technology, Norway & Bayer CropScience, Belgium |
- 14:30 Coffee break
- 14:45 Software development in bioinformatics
14:45-15:00 |
The Human Genome Variation Map Pilot Project |
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Benedict Paten University of California, Santa Cruz, USA |
15:00-15:15 |
Bionode - Modular and universal bioinformatics |
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Bruno Vieira Queen Mary University of London, UK |
15:15-15:35 |
Writing FOSS software for big biology |
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Pjotr Prins Director of Genenetwork.org, The Netherlands |
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BioInformatics and Semantic Web, what do they need a bioinformatician and a biomedical researcher? |
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Raoul Bonnal Isituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Italy |
15:35-15:50 |
Semantics for experimental protocols |
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Alexander García Universidad Politécnica de Madrid, Spain |
15:50-16:00 |
Text Mining Tools for Assisting Literature Curation |
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Chih-Hsuan Wei National Institute of Health, USA |
16:00-16:10 |
Europe PubMed Central and Linked Data |
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Jee-Hyub Kim European Bioinformatics Institute, UK |
16:10-16:20 |
LODQA: natural language interface to SPARQL endpoints |
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Jin-Dong Kim Database Center for Life Science, Japan |
- 16:20 Coffee break
- 16:40 Lightning talks (5min each)
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- Kieron Taylor
- RDF - a composable Ensembl
- Tazro Ohta
- Semantic Wet Lab: Publishing Protocols and Workflow
- Robert Hoehndorf
- Aber-OWL update
- Naohisa Goto
- BioRuby
- Shuichi Kawashima
- NBDC RDF portal
- Yasunori Yamamoto
- D2RQ mapper that gives RDF powers to RDB
- Bono Hidemasa
- AOE: All of publicly available gene expression data
- Takeshi Kawashima
- The Necessity of tools for finding out associations between phylogenetic and geologic data in modern genomic-scale phylogenetics
- Arto Bendiken
- Dydra - cloud hosting for RDF & SPARQL
- Peter Amstutz
- A brief introduction to Arvados, Common Workflow Language, and Schema Salad
- Colin Hercus
- NovoAlign, novoSort, novoLR and novoWorx
- Mark Thompson
- Open, reusable knowledge graph annotations
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- 18:00 Bus to the hackathon venue
- 19:00 Reception party
Live streaming will be available at
Video streaming by Ustream |
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