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
       Toshihisa Takagi National Bioscience Database Center, Japan
    10:10-10:30 Introduction to the 10th BioHackathon
       Toshiaki Katayama Database Center for Life Science, Japan
    10:30-11:00 Tohoku Medical Megabank Project: Large-Scale Genome Cohort Study
       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 
       Jerven Bolleman Swiss Institute of Bioinformatics (SIB), Switzerland
    11:30-12:00 10 Years of the BioHackathon and the Future
       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
       Evan Bolton National Center for Biotechnology Information (NCBI), USA
    13:40-14:00 Updates from the EBI RDF platform
       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
       Erick Antezana Norwegian University of Science and Technology (NTNU), Norway / Bayer CropScience, Belgium
    14:20-14:40 Glycomics@ExPASy
       Julien Mariethoz Swiss Institute of Bioinformatics (SIB), Switzerland 

  • 14:40 Coffee break
  • 15:20 Talks (15min + 5min for questions)
  • 15:20-15:40 Enabling practical pan-genomics with the variation graph toolkit
       Erik Garrison Wellcome Trust Sanger Institute, UK
    15:40-16:00 The Human Genome Variation Map
       Adam Novak University of California, Santa Cruz, Genomics Institute, USA
    16:00-16:20 A Graph Genome Browser
       Toshiyuki Yokoyama The University of Tokyo, Japan
  • 16:20 DBCLS 10th Anniversary Track
  • 16:20-16:40  Greetings from DBCLS director
     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
    16:40-16:45  NBDC RDF portal 
       Shuichi Kawashima Database Center for Life Science, Japan
    16:45-16:50  Umaka Suite
       Yasunori Yamamoto Database Center for Life Science, Japan
    16:50-16:55  LOD Surfer: a search tool based on class-class relationships on LOD 
       Atsuko Yamaguchi Database Center for Life Science, Japan
    16:55-17:00  SPANG: a SPARQL client for generating and reusing queries
       Hirokazu Chiba Database Center for Life Science, Japan
    17:00-17:05  Standardize experimental protocol description for reproducible science
       Tazro Ohta Database Center for Life Science, Japan
    17:05-17:10  Facilitating the use of public high-throughput sequencing data for omics research
       Hidemasa Bono Database Center for Life Science, Japan
    17:10-17:15  Linking Literature Resources with Data
       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
       Toyofumi Fujiwara Database Center for Life Science, Japan
    17:20-17:30  Questions for Lightning Talks
  • 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.
       Mark Wilkinson Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Spain
    10:05-10:20 Advancing Biomedical Knowledge Reuse with FAIR
       Michel Dumontier Institute of Data Science, Maastricht University, Netherlands
    10:20-10:40 Making GeneNetwork FAIR and creating a Journal of Open Data
       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
       Chunlei Wu The Scripps Research Institute (TSRI), USA
    11:00-11:20 Integrating Glycoinformatics with Public Web Resources
       Kiyoko F. Aoki-Kinoshita Soka University, Japan
    11:20-11:40 Linking ecological ontologies to the Sustainable Development Agenda for 2030
       Pier Luigi Buttigieg Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (AWI), Germany
    11:40-12:00 integrating microbial genome and metagenome data using semantic web technology
       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
       Konrad Karczewski Broad Institute, USA
    13:40-14:00 Clinical Deep Phenotyping and its applications
       Tudor Groza Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Australia
    14:00-14:20 Discovery over a NGLY1 deficiency knowledge graph
       Núria Queralt-Rosinach The Scripps Research Institute (TSRI), USA
    14:20-14:40 Building and Application of AMED's Genomic Variation Database
       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)
       Sebastian Burgstaller-Muehlbacher The Scripps Research Institute (TSRI), USA
    15:40-16:00 Learning from linked data, ontologies, and text
       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
       Bill Baumgartner University of Colorado Denver, USA
  • 16:20 Lightning Talks (5mins)
  • 16:20-16:25  Linked experimental protocols 
       Alexander Garcia Universidad Politecnica de Madrid, Spain
    16:25-16:30  A SmartAPI for Spontaneous Reporting Systems
       Juan Banda Stanford University, USA
    16:30-16:35  BioRuby
       Naohisa Goto Research Institute for Microbial Diseases (RIMD), Osaka University, Japan
    16:35-16:40  Bioschemas
       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
       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
       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
       Seth Carbon Lawrence Berkeley National Laboratory (LBL), USA
    16:55-17:00  Databases for RNA Expression Analysis
       David Steinberg University of California, Santa Cruz, Genomics Institute, USA
    17:00-17:05  Structured data for patient matchmaking
       Orion Buske Hospital for Sick Children (SickKids), Canada
    17:05-17:10  Linked ICGC - Cancer Genome RDF Data and its Usage
       Ryota Yamanaka Oracle Corporation Japan, Japan
    17:10-17:15  Leveraging Biomedical LOD Resources to Annotate the Function of Uncharacterized Disease-Associated Genes
       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
       Claus Weiland Senckenberg Data & Modelling Centre (SGN), Germany
    17:20-17:25  Single Cell and Linked Data
       Raoul Jean Pierre Bonnal Fondazione Istituto Nazionale Genetica Molecolare (INGM), Italy
    17:25-17:30  Questions for Lightning Talks
Live streaming will be available at