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
       Toshiaki Katayama Database Center for Life Science, Japan
    10:10-10:25 Research at the Atomic Bomb Disease Institute, Nagasaki University
       Hiroyuki Mishima Nagasaki University, Japan
    10:25-10:40 UniProt SPARQL in production
       Jerven Bolleman Swiss Institute of Bioinformatics, Switzerland
    10:40-10:55 PubChemRDF examples, potential applications, and future directions
       Evan Bolton National Center for Biotechnology Information, USA
  • 10:55 Coffee break
  • 11:10-11:25 Efforts in the semantic standardization of orthology content
       Jesualdo Tomás Fernández-Breis University of Murcia, Spain
      Applying RDF/SPARQL to ortholog databases
       Hirokazu Chiba National Institute for Basic Biology, Japan
    11:25-11:40 GlycoRDF ontology
       Thomas Luetteke Justus-Liebig University Giessen, Germany
    11:40-11:55 MeSH RDF 2015
       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
       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
       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
       Núria Queralt Rosinach Institut Hospital del Mar d'Investigacions Mèdiques, Spain
    13:45-14:00 Network Analysis and Linking for Bio2RDF
       Michel Dumontier Stanford University School of Medicine, USA
    14:00-14:15 updates
       Nick Juty European Bioinformatics Institute, UK
    14:15-14:30 YacMa: a semantic web platform for biological knowledge integration
       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
       Benedict Paten University of California, Santa Cruz, USA
    15:00-15:15 Bionode - Modular and universal bioinformatics
       Bruno Vieira Queen Mary University of London, UK
    15:15-15:35 Writing FOSS software for big biology
       Pjotr Prins Director of, The Netherlands
      BioInformatics and Semantic Web, what do they need a bioinformatician and a biomedical researcher?
       Raoul Bonnal Isituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Italy
    15:35-15:50 Semantics for experimental protocols
       Alexander García Universidad Politécnica de Madrid, Spain
    15:50-16:00 Text Mining Tools for Assisting Literature Curation
       Chih-Hsuan Wei National Institute of Health, USA
    16:00-16:10 Europe PubMed Central and Linked Data
       Jee-Hyub Kim European Bioinformatics Institute, UK
    16:10-16:20 LODQA: natural language interface to SPARQL endpoints
       Jin-Dong Kim Database Center for Life Science, Japan
  • 16:20 Coffee break
  • 16:40 Lightning talks (5min each)
    Kieron Taylor
    RDF - a composable Ensembl
    Tazro Ohta
    Semantic Wet Lab: Publishing Protocols and Workflow
    Robert Hoehndorf
    Aber-OWL update
    Naohisa Goto
    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
  • 18:00 Bus to the hackathon venue
  • 19:00 Reception party

Live streaming will be available at

Video streaming by Ustream