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Maciek Smuga-Otto edited this page Feb 23, 2016 · 27 revisions

Welcome to the 2nd RDF summit Wiki!


  • Dates: Feb 19-24, 2016
  • Venue: Tohoku Medical Megabank Organization (ToMMo), Tohoku University, Miyagi, Japan
  • Accommodation: Hotel Monte Hermana Sendai (see detailed directions)
  • Host: Database Center for Life Science (DBCLS)
  • Co-host: Tohoku Medical Megabank Organization (ToMMo)


In collaboration with the Tohoku Medical Megabank Organization, the Database Center for Life Science is exploring possibilities to utilize the reference genome graph technology to handle Japanese genomes. We worked on the development and standardization of the Semantic Web technologies in genome/sequence annotations in DDBJ/ENA/GenBank and Ensembl during the 1st RDF summit. Therefore, it would be ideal to integrate those two graphs (sequence variations and semantic knowledge) for the future applications in life sciences.

Tentative topics for the 2nd RDF summit may include (but not limited to):

  • Try to deploy the reference genome graph method to Japanese genome data
  • Discuss and develop up/down-stream tools for utilizing the genome graph in production
  • Standardize the best way to semantically represent and use reference genome graph with annotations
  • and any relevant issues raised by participants


  • Feb 18: Arrival to Japan
  • Feb 19:
    • 9:00 Gather at the hotel lobby
    • 10:00-12:00 Seminar at ToMMo
    • 13:00-18:00 Hackathon 20160219
  • Feb 20:
  • Feb 21:
  • Feb 22:
  • Feb 23:
    • 10:00-18:00 Hackathon 20160223
    • 13:00-18:00 Wrap-up
    • 18:00- Party?
  • Feb 24: Departure from Japan
    • 9:00-12:00 Meeting (not mandatory)



  • Erik Garrison (Sanger, UK) - vg
  • Jouni Siren (Sanger, UK) - GCSA2
  • Adam Novak (UCSC, US) - reference genome graph
  • Maciek Smuga-Otto (UCSC, US) - reference genome graph server
  • Orion Buske (Univ of Toronto, Canada) - Match Maker Exchange, PhenomeCentral
  • Jerven Bolleman (SIB, Swiss) - UniProt RDF, FALDO
  • Kieron Taylor (EBI, UK) - Ensembl


  • Soichi Ogishima (ToMMo, Japan)
  • Hajime Suzuki (Univ of Tokyo, Japan)
  • Kana Shimizu (AIST, Japan)
  • Shin Kawano (DBCLS, Japan)
  • Atsuko Yamaguchi (DBCLS, Japan)
  • Shuichi Kawashima (DBCLS, Japan)
  • Toshiaki Katayama (DBCLS, Japan)


  • Soichi Ogishima (ToMMo, Japan)
  • Toshiaki Katayama (DBCLS, Japan)
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