Skip to content

Home

Jump to bottom Edit New page
Yasunori edited this page May 19, 2014 · 28 revisions

Welcome to the RDF summit 2014 Wiki!

Objectives

We, in DBCLS, have been developing the TogoGenome application which utilizes RDF versions of RefSeq, UniProt and other resources with Identifiers.org URIs, FALDO and some standard/in-house developed ontologies. Currently, TogoGenome covers complete genomes of prokaryotes and it can successfully summarize annotations stored in our SPRAQL endpoint thanks to the JBrowse and our TogoStanza framework. We will extend our system to support human and other eukaryotes soon.

In parallel, we believe Ensembl RDF will be a great resource to be widely used when released. However, we anticipate that we'd better to make an agreement on the design of RDF models, URIs and ontologies used in the Ensembl RDF as which can be a de facto standard of the RDF representation of genome annotations. Potentially, the RDF version can replace a variety of existing standard protocols and file formats including DAS/GFF/GTF/GVF/VCF etc. in the near future, so we think it is essential to have a community agreement on how to mutually represent sequence annotations in RDF among those file formats, INSDC sequence records and Ensembl RDF before their initial release.

Based on the discussions during the past BioHackathons, we hope to discuss on the following points

  • common RDF models (e.g., how to represent genes, transcripts, exons and other sequence annotations)
  • common URI schema (e.g., how to identify the reference sequence with a version and link to external resources)
  • common ontologies (e.g., how to describe genome annotations with FALDO locations, SO types, INSDC/DDBJ features etc.)

and develop a standard guideline so that we can easily share/merge sequence annotations in RDF. If the guideline is widely accepted, third party groups can easily provide their annotations to be integrated and/or develop tools for mutually converting legacy data formats to RDF, aggregating sequence annotations, and applications on top of them. Additionally, we are facing with an urgent need to support personal genomes and clinical information which must be securely accessed. Therefore, following options can be discussed in the next NBDC/DBCLS BioHackathon (mid November 2014) based on our efforts in the RDF summit.

  • develop common tools to convert non-RDF data (e.g., BioInterchange toolkit, Open Bio*)
  • future plans on handling personal genomic data and clinical information (e.g., security issues)

Program

  • May 16: arrival in Japan
  • May 17: meeting at DBCLS 10:00-18:00 (gather at the hotel lobby by 9:30 AM)
  • May 18: meeting at DBCLS 10:00-18:00 + BBQ?
  • May 19: meeting at DBCLS 10:00-18:00 + deep Tokyo night
  • May 20: meeting at DBCLS 10:00-18:00 or visit NIG for INSDC pre-meeting?
  • May 21: departure from Japan

Venue

  • Akihabara Washington Hotel, close to Akihabara station
  • DBCLS, close to Kashiwanoha-campus station of Tsukuba Express (TX) line, 6th floor of the Kashiwanoha satellite of the University of Tokyo building

Access

Participants

International:

  • Kieron Taylor (EBI/Ensembl group, UK) - Ensembl RDF
  • Simon Jupp (EBI/RDF group, UK) - Ensembl RDF
  • Camille Laibe (EBI/Identifiers.org group, UK) - URI standardization
  • Jerven Bolleman (SIB/UniProtKB/Swiss-Prot, Switzerland) - UniProt/FALDO
  • Michel Dumontier (Stanford/NCBO, US) - Bio2RDF, HCLS DB metadata
  • Joachim Baran (Stanford/NCBO, US) - BioInterchange, GFVO, BaseSpace
  • Raoul Bonnal (INGM, Italy) - Open Bio*, BaseSpace, Horizon 2020

Domestic:

  • Takatomo Fujisawa (NIG/DDBJ) - INSDC RDF
  • Soichi Ogishima (Tohoku Univ/Medical megabank) - personal genome
  • Hiroyuki Mishima (Nagasaki Univ) - UCSC API, human genetics
  • Shin Kawano (DBCLS) - cancer genome
  • Tazro Ohta (DBCLS) - SRA
  • Shuichi Kawashima (DBCLS) - TogoGenome
  • Toshiaki Katayama (DBCLS) - TogoGenome, BaseSpace
Add a custom footer
Add a custom sidebar
Clone this wiki locally