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23 Biohackathon-presentation.pdf

Application of RDF-based models and tools for enhancing interoperable use of biomedical resources

Representative: Toshiaki Katayama



Database Center for Life Science (DBCLS), Japan


  • Hirokazu Chiba
  • Toshiaki Katayama
  • Tazro Ohta
  • Shuichi Kawashima
  • Atsuko Yamaguchi
  • Toyofumi Fujiwara

Background information

DBCLS has contributed to developing RDF-based data models and tools collaborating with biomedical researchers. Recent activities include construction of Med2RDF datasets and collaboration on BioSamples with EBI. Cross-institutional application of these models is important toward interoperable use of distributed biomedical resources. In addition to the data modeling, we have contributed to providing datasets as NBDC RDF portal service, which will be useful as a data integration platform. For effective use of RDF databases, we have developed Semantic Web tools, including LOD Surfer, SPANG, SPARQList, and TogoStanza. Application of these tools should be addressed for enhancing interoperable use of distributed biomedical resources.

Expected outcomes

  • Development of applications using Med2RDF datasets
  • Interoperable use case of BioSamples model
  • Use case of NBDC RDF portal as FAIR data
  • Application of LOD Surfer
  • Application of SPANG
  • Application of SPARQList
  • Application of TogoStanza

Expected audience

Developers using RDF/SPARQL/JavaScript, ontologists, biomedical researchers

Expected hacking days: 4 days

Related works and references

GitHub or any other public repositories of your FOSS products (if any)


  • Toshiyuki Yokoyama (University of Tokyo)
  • Manabu Ishii (RIKEN)
  • Ryota Yamanaka (Oracle)
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