Public symposium of the BioHackathon 2017 will be held at the JST Science Plaza in Tokyo on Sep 9-10th.
Note for speakers: Please try to leave few minutes for Q&A within a given slot (except for lightning talks).
September 9th (Sat)
- 8:30 Meet up at the hotel lobby
- 9:00 Registration opens / Coffee
- 10:00 Introduction and special talks
10:00-10:10 |
Welcome address |
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Toshihisa Takagi National Bioscience Database Center, Japan |
10:10-10:30 |
Introduction to the 10th BioHackathon |
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Toshiaki Katayama Database Center for Life Science, Japan |
10:30-11:00 |
Tohoku Medical Megabank Project: Large-Scale Genome Cohort Study |
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Atsushi Shimizu Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Japan |
11:00-11:30 |
UniProt: a decade on the semantic web, challenges and successes |
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Jerven Bolleman Swiss Institute of Bioinformatics (SIB), Switzerland |
11:30-12:00 |
10 Years of the BioHackathon and the Future |
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Panel discussion Panelist: TBA |
- 12:00 Lunch
- 13:20 Talks (15min + 5min for questions)
13:20-13:40 |
Advances in PubChem data linking: towards knowledge discovery |
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Evan Bolton National Center for Biotechnology Information (NCBI), USA |
13:40-14:00 |
Updates from the EBI RDF platform |
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Thomas Liener European Bioinformatics Institute (EMBL-EBI), UK |
14:00-14:20 |
Agrisemantics: harnessing the Semantic Web technologies for the benefit of Agriculture, Food and Nutrition |
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Erick Antezana Norwegian University of Science and Technology (NTNU), Norway / Bayer CropScience, Belgium |
14:20-14:40 |
Glycomics@ExPASy |
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Julien Mariethoz Swiss Institute of Bioinformatics (SIB), Switzerland |
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- 14:40 Coffee break
- 15:20 Talks (15min + 5min for questions)
15:20-15:40 |
Enabling practical pan-genomics with the variation graph toolkit |
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Erik Garrison Wellcome Trust Sanger Institute, UK |
15:40-16:00 |
The Human Genome Variation Map |
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Adam Novak University of California, Santa Cruz, Genomics Institute, USA |
16:00-16:20 |
A Graph Genome Browser |
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Toshiyuki Yokoyama The University of Tokyo, Japan |
- 16:20 DBCLS 10th Anniversary Track
16:20-16:40 |
Greetings from DBCLS director |
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Yuji Kohara Database Center for Life Science, Japan
Asao Fujiyama Research Organization of Information and Systems, Japan
Susumu Goto Database Center for Life Science, Japan
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16:40-16:45 |
NBDC RDF portal |
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Shuichi Kawashima Database Center for Life Science, Japan |
16:45-16:50 |
Umaka Suite |
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Yasunori Yamamoto Database Center for Life Science, Japan |
16:50-16:55 |
LOD Surfer: a search tool based on class-class relationships on LOD |
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Atsuko Yamaguchi Database Center for Life Science, Japan |
16:55-17:00 |
SPANG: a SPARQL client for generating and reusing queries |
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Hirokazu Chiba Database Center for Life Science, Japan |
17:00-17:05 |
Standardize experimental protocol description for reproducible science |
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Tazro Ohta Database Center for Life Science, Japan |
17:05-17:10 |
Facilitating the use of public high-throughput sequencing data for omics research |
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Hidemasa Bono Database Center for Life Science, Japan |
17:10-17:15 |
Linking Literature Resources with Data |
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Jin-Dong Kim Database Center for Life Science, Japan |
17:15-17:20 |
PubCaseFinder: a diagnosis assistant tool for rare diseases using published case reports |
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Toyofumi Fujiwara Database Center for Life Science, Japan |
17:20-17:30 |
Questions for Lightning Talks |
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- 17:30 Group photo, Move to the Reception venue
- 18:00 Reception Party
September 10th (Sun)
- 9:00 Registration opens / Coffee
- 9:30 Announcements
- 9:40 Talks (15min + 5min for questions)
9:40-10:05 |
Hacking Data Interoperability - FAIR outcomes from BioHack 2015 & 2016. |
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Mark Wilkinson Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Spain |
10:05-10:20 |
Advancing Biomedical Knowledge Reuse with FAIR |
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Michel Dumontier Institute of Data Science, Maastricht University, Netherlands |
10:20-10:40 |
Making GeneNetwork FAIR and creating a Journal of Open Data |
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Pjotr Prins University Medical Center Utrecht, Netherlands & University of Tennessee Health Science Center, US |
10:40-11:00 |
BioThings and SmartAPI: building an ecosystem of interoperable biological knowledge APIs |
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Chunlei Wu The Scripps Research Institute (TSRI), USA |
11:00-11:20 |
Integrating Glycoinformatics with Public Web Resources |
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Kiyoko F. Aoki-Kinoshita Soka University, Japan |
11:20-11:40 |
Linking ecological ontologies to the Sustainable Development Agenda for 2030 |
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Pier Luigi Buttigieg Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (AWI), Germany |
11:40-12:00 |
MicrobeDB.jp: integrating microbial genome and metagenome data using semantic web technology |
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Hiroshi Mori National Institute of Genetics, Japan |
- 12:00 Lunch
- 13:20 Talks (15min + 5min for questions)
13:20-13:40 |
The ExAC Browser: Displaying reference data information from over 60,000 exomes |
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Konrad Karczewski Broad Institute, USA |
13:40-14:00 |
Clinical Deep Phenotyping and its applications |
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Tudor Groza Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Australia |
14:00-14:20 |
Discovery over a NGLY1 deficiency knowledge graph |
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Núria Queralt-Rosinach The Scripps Research Institute (TSRI), USA |
14:20-14:40 |
Building and Application of AMED's Genomic Variation Database |
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Hiroyuki Mishima Nagasaki University, Japan |
- 14:40 Coffee break
- 15:20 Talks (15min + 5min for questions)
15:20-15:40 |
Citation Graph Visualization, or how to tackle the publication avalanche (with Wikidata) |
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Sebastian Burgstaller-Muehlbacher The Scripps Research Institute (TSRI), USA |
15:40-16:00 |
Learning from linked data, ontologies, and text |
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Robert Hoehndorf King Abdullah University of Science and Technology (KAUST), Saudi Arabia |
16:00-16:20 |
Integrating text-mined assertions into the Knowledge Base of Biology |
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Bill Baumgartner University of Colorado Denver, USA |
- 16:20 Lightning Talks (5mins)
16:20-16:25 |
Linked experimental protocols |
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Alexander Garcia Universidad Politecnica de Madrid, Spain |
16:25-16:30 |
A SmartAPI for Spontaneous Reporting Systems |
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Juan Banda Stanford University, USA |
16:30-16:35 |
BioRuby |
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Naohisa Goto Research Institute for Microbial Diseases (RIMD), Osaka University, Japan |
16:35-16:40 |
Bioschemas |
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Leyla Jael Garcia Castro European Bioinformatics Institute (EMBL-EBI), UK |
16:40-16:45 |
Storing and Querying Evolutionary Relationships Among Millions of Genes in the Orthologous Matrix (OMA) Using RDF |
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Tarcisio Mendes de Farias University of Lausanne (DEE - UNIL) / Swiss Institute of Bioinformatics (SIB), Switzerland |
16:45-16:50 |
minialign: fast and accurate alignment tool for PacBio and Nanopore long reads |
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Hajime Suzuki Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Japan |
16:50-16:55 |
Noctua, models, and the greater web |
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Seth Carbon Lawrence Berkeley National Laboratory (LBL), USA |
16:55-17:00 |
Databases for RNA Expression Analysis |
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David Steinberg University of California, Santa Cruz, Genomics Institute, USA |
17:00-17:05 |
Structured data for patient matchmaking |
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Orion Buske Hospital for Sick Children (SickKids), Canada |
17:05-17:10 |
Linked ICGC - Cancer Genome RDF Data and its Usage |
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Ryota Yamanaka Oracle Corporation Japan, Japan |
17:10-17:15 |
Leveraging Biomedical LOD Resources to Annotate the Function of Uncharacterized Disease-Associated Genes |
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Tiffany Callahan University of Colorado Denver | Anschutz Medical Campus (AMC), USA |
17:15-17:20 |
Deep Learning to mobilize trait data from multimodal data sources |
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Claus Weiland Senckenberg Data & Modelling Centre (SGN), Germany |
17:20-17:25 |
Single Cell and Linked Data |
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Raoul Jean Pierre Bonnal Fondazione Istituto Nazionale Genetica Molecolare (INGM), Italy |
17:25-17:30 |
Questions for Lightning Talks |
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Live streaming will be available at
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